Strange.
As far as I remember, it should autodetect Valve 220 maps, and the Q1 rotation stuff should only be necessary to make things line up as expected, not ungarble UVs completely.
Can you pastebin (a section of) the map with the problem so I can test it locally? (with a list of expected texture sizes)
Thanks for the reply, here's a small hallway.
https://pastebin.com/GVxfj6S9
All textures sizes are at 256x256, let me know if this works.
My current workaround has been to build the map in valve mode, and convert the map format to standard, which keeps thing mostly intact. Obviously there's a few texture alignment snags here and there, but a price I'm more than willing to pay to continue using hammuer. It's a great tool!
Bringing this up to confirm that by converting to standard, this test section also imports correctly.