If I can just add that you cant just install any 040 library. It has to be from phase5 to work propery on the blizzard boards. If its commodores own or for the Apollo cards, it will cause the effect you describe
Also you can use blizkick to remove the flash version by using the bppcfix040 module as part of the blizzkick command line. Then setpatch will load the version stored in libs: folder as apposed to the one that would already be resident in memory without bppcfix.