Thanks for the replies!
@Asmusr, I tried removing the ,x options. The compile errors went away but only one ~8k levelx-rom file was created per asm file, so later parts of the makelevels.bat file failed.
@PeteE I changed the aorg >6000,x directives to be separate aorg >6000 and bank x directives as you suggested, which also compiled fine, but I was greeted by a clear screen and random noise when I pressed 2 for Tiger Shark on the TI menu screen.
Now that I know about the bank directive, I looked it up in the xdt99 manual at https://github.com/endlos99/xdt99/blob/master/doc/MANUAL.md#banked-output. Based on the documentation, I tried changing "aorg >6000,0" to "bank all, >6000" and the remaining occurrences of aorg to "bank 1", "bank 2" etc. This also compiled okay, but the resulting files were around 15K each instead of 8k, and the same clear screen and random noise was seen when I tried to launch the cart.
My last attempt was changing "aorg >6000,x" to "bank x, >6000" and not having a bank all directive. This change got the output files back down to 8K each, but still with the same results.
One other difference to note - the output files no longer contain the base address as part of the file name. For example, "level1-rom_6000_b1" is now being named "level1-rom_b1". Any idea if that is expected with the bank directive or if it indicates I've done something incorrectly?
I may punt on this for now. Trying to fix this is way above my expertise currently. I only tried building Flying Shark to confirm I had installed everything correctly. I can't even claim to know enough to be dangerous yet! Thanks again for the quick responses!