I haven't seen this one anywhere in the open bugs. It does not seem to be "ultimate undo weirdness":
I use jEdit as a preferred editor to edit websites, but some time back (either 4.3.2 was the last that worked, or where it started), it got so all I had to do is open any file, edit it for a while (this varies, 1-20 min.), and without fail, four things would all happen about the same time:
1) undo quits working; generating an error instead
2) jEdit started running a little slow, like it was bogged down
3) adding lines of text in a document did not extend the end of the buffer as far as the scrollbars or cursor was concerned. i.e., saving the document and restarting jEdit would produce the full document, but before doing that, I could not scroll to the end fully.
4) although this may or may not have happened predictably, scrolling off the screen with the cursor would not manage to keep the cursor on the screen. the position of the view of the buffer would remain unchanged. The scrollbar would work normally, and one could find the cursor, but as above, if the size of the file had increased, it was impossible to scroll to see the very bottom.
Closing and reopening jEdit always fixes it - temporarily. This happens on large and on small files. I typically have several tabs open; as well as the Project Viewer. I have disabled as many plugins as I feel comfortable while still keeping the ones I use. Those still enabled were: BufferTabs, Clipper, Common Controls, Error List, JDiff, Project Viewer, SuperAbbrevs, Text Tools & Vox Spell.
This has been happening either since or immediately after 4.3.2, for all the stable distributions. I am currently trying 5.0pre1, which seems to run fine except that it has this problem too. This bug happens on Remix_OS 64-bit Linux (although I couldn't guarantee if it was the Oracle or open source JRE); as well as WinXP Home SP3 32-bit, under both the standard Oracle JRE and my favorite, JRockit. I have an Athlon X2 CPU.
I really like jEdit, and am sorry to lose undo and other sane behavior so frequently. To my taste, it is the best free HTML/PHP editor out there, with the possible exception of gedit, which currently runs very poorly on Windows. Hope this info helps, as it is, to my mind, the biggest bug in jEdit I am aware of.