The following issues are known to exist in FQM:

[2/17/05 2:40 PM PST] Selecting a Bad homeworld start is always a bad idea. It will often lead to some player's having a homeworld that is a huge, large, etc. sized planet rather than small. This planet will have type and atmosphere that does not match the race in question. This is caused by a quirk in how SE4 chooses homeworlds. You can avoid any such problems by always using an Average or Good planet start setting.

[8/12/05 10:00 AM PST] The first release of FQM Deluxe 2.10 and FQM Standard 1.23 included an error involving many warp points having an ability label that they should not have. This has been fixed. If you downloaded FQM Deluxe 2.10 before this date, you can simply apply this Deluxe WP Fix to your current installation. If you downloaded FQM Standard 1.23 before this date, you can simply apply this Standard WP Fix to your current installation. There is no need to redownload the entire mod again.

[10/04/05 12:00 PM PST] When generating a map in the Map Editor, you will likely get an error dialogue like: "Access violation adress 000471C53 in module 'se4map.exe' read of adress 00007269." The Map Editor is not very good at using modded data files, so it tends to crash on them when generating random maps. The only way to use a randomly generated map with FQM in the Map Editor is to generate the map in-game, save it to a file, and load it in the editor. Note that the Map Editor has no problems with using modded data files for manually creating and editing maps, only with quadrant generation.