CRITICAL BUG: PDF pages flash briefly and then go blank

I’m running into an issue with MarginNote 4—version 4.1.21 (20006)—where pages of PDFs suddenly go blank. The page’s content flashes briefly as I page to the next page, and then the page goes blank. I’ve tried all sorts of combinations, external folders, importing PDFs into MarginNote, etc. Restarting MarginNote does not help, neither does rebooting macOS.

This is happening on an M1 Pro 16" MacBook Pro, 32GB RAM, running macOS Sequoia 15.6.

I was using MarginNote to present and navigate through material used in a recent programming training session and was deeply embarrassed when the pages started disappearing. Until this is fixed I am forced to use Preview.

Please fix this urgently / prioritize this, as it’s an absolute deal-breaker.

Worth mentioning that I just updated to v 4.1.22 and the same issue is present.

The “flashing and then disappearing” page issue occurs most frequently when MarginNote 4’s window is large (that is, filling the entire screen, on my 27" Apple Studio Display, but not in Full Screen mode). If I resize Margin Note’s window to be smaller, then the blank page/s suddenly render properly. See the two attached screenshots:


Further experimentation shows that when Margin Notes’s window height crosses a certain threshold (about 70% of the monitor size), then the pages disappear, but if I resize it so the window is shorter (vertically) then pages reappear. See screenshots


Finally (at least for tonight), I’ve tried cleaning / decompressing / decompressing, etc. my PDF files using mutool but that has no effect, so this isn’t an issue with my PDFs but rather a bug in Margin Note. Preview has no problem at all with any of the PDFs (whether I’ve “cleaned” / decompressed / etc. them or not).

See mutool: all purpose tool for dealing with PDF files ∙ mupdf Commands ∙ Man Pages ∙ ManKier for reference.

Hello, we will analyze this issue immediately. We are truly sorry for the less-than-ideal experience you’ve had.

If only some of your PDF documents are having the above-mentioned issues, as an emergency solution, you can try converting your PDF into an image-only PDF and then give it another try.

Image-only PDFs are a (rather brutal) last resort… image-only PDFs will remove the ability to generate a mind-map from the TOC, and I will be better served in today’s 2.5-hour training session simply using Preview.

Thank you for your attention to this… I hope for a solution as soon as possible. I truly love Margin Note, but this bug has shaken my confidence in the product (very) badly.

Any feedback / progress on resolving this bug? This is still affecting me—tried again this morning to identify the situations that cause it, and it (mostly) appears when MarginNote’s window is sized to fill the monitor (but not necessarily in Full Screen mode—though the “pages flash then go blank” issue occurs in Full Screen mode as well).

@Adeline: This is getting completely stupid. As of this afternoon MarginNote is now showing blanks for all pages in a set if ITIL PDFs I’ve been working through. Preview and Adobe Acrobat Reader (the only other two PDF viewers I’ve tested) all work perfectly, while MarginNote is showing blank pages for every single page. This is a complete show-stopper.

May I respectfully ask that this receive high and immediate attention? I have paid good (and fairly substantial) money to unlock Max edition—which I use on my iPad as well as Mac—and right now MarginNote is not only completely and utterly useless to me, but is causing great frustration. I cannot continue like this and am now close to switching to Heptabase, despite its high price.

I appreciate your attention.

The attached screen-recording (MP4) shows the issue:

If the MarginNote window is made small, then it (mostly) renders PDFs fine, but the moment the window size is increased, MarginNote dies miserably.

I just downloaded MarginNote 3 from the App Store (yes, I was a MarginNote 3 user who fell into the MarginNote 4 trap :cry:) and MarginNote 3 works perfectly, so this is not a bug in macOS or some Apple Silicon-related issue, but is a MarginNote 4 problem.

:warning: For anyone reading this thread, I strongly discourage upgrading to MarginNote 4 if you are in the middle of research or need a tool you can rely on, and would recommend sticking with MarginNote 3—at least until this bug is fixed. MarginNote 4 has some beautiful features, but they are all completely worthless if you can’t see the pages of the book/s you’re studying…

Hello, we suspect that this might be related to insufficient cache on your device. You can try clearing the background apps and freeing up storage space.

Hi @Adeline,

I have plenty of storage:

> df -h /
Filesystem        Size    Used   Avail Capacity iused ifree %iused  Mounted on
/dev/disk3s3s1   926Gi    10Gi   378Gi     3%    426k  4.0G    0%   /

The machine is an M1 Max MacBook Pro 16" (2021), has 32GB, running macOS Sequoia 15.6 (24G84).

I have cleared MarginNote 4’s cache (“temporary storage”), cleared system caches, rebooted, etc.—all to no avail.

MarginNote 3 does not have this problem, only MarginNote 4, so this—to my mind, at least—not caused by a system issue, insufficient cache, etc.

The attached screenshots show that MarginNote 3 has no problems, but MarginNote 4 shows blank pages when the window is “tall” but (mostly) renders correctly when the window is “short”.

MarginNote 3 – No problems:

MarginNote 4 – Fine if the window is “short”:

MarginNote 4 - Blank pages if window is tall:


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To your point on “insufficient cache” and “clearing the background apps”, I have rebooted and launched only MarginNote 4 and still have this issue. I’m done with MarginNote 4 now as this is a huge waste of my time, which is in short supply, and will stick with MarginNote 3 until such time as you folks are able to provide a fix.

Fellow architects—and not a few of whom I mentor—have, over the years, asked me “What are the tools you use to study”, and I’ve always recommended MarginNote. However, I can no longer do so (at least, not until this massive bug is resolved).

@Adeline: Do you have any ETA (or sense of a possible ETA) to get this fixed? I have just, painstakingly, restored all of my Keyboard Maestro macros—which I had updated to work with MarginNote 4’s menus and keyboard shortcuts—to work with MarginNote 3. MarginNote v4 is a much better product (to my mind) than v3 (assuming, of course, that it actually renders PDFs), and I would prefer to use v4 than v3. For now, though, I have no other option but to use v3 (or switch to Heptabase).