From what I remember:
Valve changed HL1 to include support for Linux
To do this, they entirely changed the HL1 directory. You may have noticed your GCF doing a 100% change update some time ago.
I believe this means DLLs need rewriting, or that directories need placing elsewhere. Vic may have more up-to-date news on this.
For SP mods I'd recommend people revert back to their WON installs (eww) or use Xash.