1964 0.9.9 and corrupted save files

Recently, I've been running into problems with 1964 creating corrupted saves, both mempack1.mpk and [GameName].fla. I generally prefer to use the in-game save system instead of Save States, but because of this problem, I'm beginning to change my mind.

Is this a known problem with 1964 0.9.9?

The problems I've had were on two different machines:
Athlon 1Ghz
384MB RAM
Radeon 9000 Pro 128MB w/ latest ATI drivers
RiceVideo 5.5.0b2 w/ DirectX and Pixel Shader engine
schibo's audio
RSP Plugin

Pentium 4 2Ghz
512MB RAM
GeForce 2 MX/MX-400 32MB w/ latest nVidia drivers
RiceVideo 5.5.0b2 w/ DirectX and To Fit Your Video Card option
schibo's audio
RSP Plugin

To be honest, I've only had the problem on one game on each system:

Athlon 1Ghz
384MB RAM
Radeon 9000 Pro 128MB w/ latest ATI drivers
RiceVideo 5.5.0b2 w/ DirectX and Pixel Shader engine
N-Rage's DirectInput8 V2.1.80a (came with 0.9.9)
schibo's audio
Shadowgate 64 - Trials of the Four Towers (U) [!]
- Generates an "Exception in Emulation Thread" when game loads using RiceVideo 5.5.0b2 (and locks up when entering the park room in 5.4.3) until the first Mempack file is deleted.

Pentium 4 2Ghz
512MB RAM
GeForce 2 MX/MX-400 32MB w/ latest nVidia drivers
RiceVideo 5.5.0b2 w/ DirectX and To Fit Your Video Card option and Enable SSE
schibo's Audio Plugin 1.2 (came with 0.9.9)
N-Rage's DirectInput8 V2.1.80a (came with 0.9.9)
RSP Plugin (taken from Project 64 1.0.5sp1, required to get audio in Paper Mario)
Paper Mario (U) [!]
- Generates an "Exception in Emulation Thread" when you try to save at a save block until PAPER MARIO-65EEE53AED7D733C.fla is deleted.

I'm using the Pentium 4 now because the AMD system's motherboard seems to have shorted out (system acts like it has no power in two different cases).

Seeing as how Paper Mario was the first game I played using 1964 0.9.9 on the Pentium 4 system, I was concerned that this might be some sort of flaw in the emulator itself.

I found out how to corrupt a Paper Mario save file (at least in my emulator configuration):
Save a state, then save the game at an S block, then reload the saved state.
It might also require you trying to save at the S block again. Boom, it will crash every time you try to save.