I'm not sure if this is already a known issue reported elsewhere, but I wanted to bring it up just in case. This is beyond stupid and I honestly don't know what's going on here. For the record, this is the latest Sonic 1 GitHub disassembly targeting the AS branch.
When game format is set to Sonic 1:

When set to Sonic 2:

If I had to guess, Flex 2 doesn't like the new map macros used for the DPLCs, because when I copy-paste the raw byte data from the outdated ASM68K branch, it loads fine with game format set to Sonic 1.
This is a huge problem to anyone new to the software, cause would they know to set their game to the incorrect format to fix this arbitrary issue? Would love a fix ASAP.