Some more things I've found out while using 3.0b12:
-If the target game is set to black/white, the experience/level of the Pokemon doesn't match. for example, the default level I've found to be put every time I create a new pokemon (or reset controls from the tools menu), the level is set to 100 but the experience is 0. The game treats the pokemon as lv. 1.
("sub-issue" from the previous)-If you import a Pokemon from an older game, (through the method you told me, which is set the game to hgss, import and then change to bw), the experience is set to be 1 lv higher than the lv the pokemon was (if it's lv. 100, it loops to lv. 1). for example, a lv 5 jirach,i imported with hgss set as the game, has 156 exp and lv 5. However, once I change the target game to B/W, it bumps up to 270, but the program still says it's lv. 5, and the game takes the pokemon as being at lv, 6. This can be easily rectified by rewriting the desired level of the pokemon (for both cases).
-Sometimes the program doesn't let you choose the nature of a pokemon, even if you erase its pid or reset controls (from the tools menu). The program needs to be closed first then reopened to workaround this problem.
---(edit: possibly handy info regarding the previous issue). This seems to happen if you load a pokemon from a file into pokegen and then change the pokemon. The nature is grayed out, even if you erase the pid or even try to change it)
-If the right click menu (for setting pokemon in the boxes/party) is repeatedly used, sometimes it will stop working (that is, not appearing). The only workaround is to close and reopen the program.
-In a reply to my previous post regarding the PID Finder not setting the IVs, nature, shininess etc, saying that I had to select the one I wanted, then click ok, it still doesn't work. Maybe it's me doing something wrong? (It worked in past versions with that method, that's why I came back with this question)
That is all for now. I'll keep reporting any issues I find while using the program. I apologize if there are any typos in my posts.