NB! The fixes, described below, apply only to e-mail client shipped with PR1 2. PR1.3 already has all those problems solved.

I did put together a custom version of modest, to fix some bugs that PR1.2 introduced: send/receive and email notifications not working with POP3 accounts and messages deleted from server regardless of "Leave messages on server" setting.
Latter was fixed in git already, for former I had to come up with some patches. I did make some performance improvements too, to reduce the time it takes to check for messages: original version checked 3 times in a row when send/receive button was pressed in headers window Now it does it only once.

The patched version, which is in attachment, is based on http://gitorious.org/modest/modest modest-3.4 branch. To install, copy this file to N900, become root and unpack it:
This will overwrite /usr/bin/modest.launch and /usr/lib/camel-lite-1.2/camel-providers/libcamelpop3.so. Reboot your phone.

To uninstall, just reinstall modest and libcamelpop3 from PR1.2:
I have tested it with my POP3 and gmail accounts and it seems to be working fine, but I cannot give any guarantees, use at your own risk.