I wouldn't recommend the installer either as it destroys the startup-sequence. Make a backup of startup-sequence and user-startup (just to be on the safe side) before installing.
Actually it asks whether you want startup-sequence replaced automatically. If you choose yes, it makes a backup automatically first. If you choose no, it just tells you what changes to make and brings up a text editor so you can make the changes yourself.
However, my site
http://amigan.1emu.net is down, so getting a copy of the latest BB3&4 (V1.0i) may be difficult, try
https://web.archive.org/web/20150209153516/http://amigan.1emu.net/releases/ Hopefully my site will be back up soon, probably at a different URL though...
@alienkidmj12:
More details needed: (a) what libraries is it failing to open? (use SnoopDOS if it won't tell you) and (b) did this issue start happening at the time BB3&4 was installed or later on (sounds like later on, which would suggest the issue isn't caused by BB3&4)?