I can see what you are reporting. The debug log notes this:
Detected C:\classic99\Contributors\Harry_Wilhelm\Compiler256D\QD as a V9T9 file
loading 0xA3E bytes
VDP disk buffer header corrupted at PC >FD0E
DSR opcode >5 on PAB >0FEE, filename DSK1.AS
Invalid file buffer header at >37D7. Bytes >AA,>40,>07,>11,>03
So at the "top of ram" pointer, there needs to be a 6 byte header for the TI disk controller to function. Before a DSR call, Classic99 checks whether this header is at least somewhat sane:
1) the first byte must be >AA (although it's not clear that the disk controller checks this)
2) the next two bytes are the top of VRAM. It's expected to remain >3Fxx. You can see here it was changed to >4007
3) the fourth byte is the CRU of the controller in question, >11 is correct, Classic99 only supports >11
4) the final byte is the number of files, Classic99 just ensures it's 9 or less (ie: it doesn't check if all the file buffers would fit)
So that leads to two questions:
-why did FW change the top of VRAM to an invalid value? and
-does anyone care?
We can see the PC it changed at... breakpointing there shows a copy loop, which it looks like Funnelweb is using to copy PABs into VDP.. but what's very odd is that exact sequence above is deliberately copied overtop of the DSR header. So that's the 'why', as far as can be determined.
For the 'who cares', I did a search through the disk controller disassembly. This value does actually matter, it's used to locate structures inside the reserved space... one of the reasons for this check was the pCode card crashing in odd ways when it was incorrect (even on the Classic99 controller which doesn't technically need it).
So, I gave it a shot on the real TI controller, and it does in fact succeed despite the bad pointer. I guess it's never inspired to call the setup routine that has trouble with it.
Best I can do is make it an option. I put it in there to help with all the disk access issues that everyone (including me) keep running into, to help pinpoint where the issues occur. But since some people don't care, I guess I don't need to enforce it.