Hmm.... are you loading a state? I played it, and that happened to me once when I loaded. Not really sure why. If you restart the emu, it shouldn't happen again.
Looks like you patched SP1 on top of PJ64 1.4, because SP1 does not update pj64.exe it will not improve compatibility for 1.4, this is exactly what happens with 1.4. download version PJ641.5