LCModel execution taking significant time

Hm. It’s odd that the GUI runs but the core binary doesn’t.

I’d suggest you try re-compiling the LCModel binary from source (see instructions here and discussion here); note that you can also compile the source directly for Windows/Mac so you don’t have to go the extra mile via WSL. The only downside is that you can’t use the GUI (which is not provided in source), but honestly it’s awfully clunky anyway, and I strongly recommend not using it in the first place, but rather to learn to write valid control files (see LCModel manual Section 5.3) which makes batching a lot easier.