I can only reproduce this issue if I run the Remaster with the modified shaders in fullscreen mode. It could still be that only the combination of Taurus and the shaders brings that about, but it sounds rather farfetched to me. For a test, the runtime modifications to the EXE could be disabled through DISABLE_EXE_RUNTIME_MODS in GlobalDefinesAlt.xml. Unfortunately, I'm not sure that I ever tested that XML setting (I might have), so this test won't bring full assurance. One could also check if the problem already occurs in pre-Taurus versions of the Remaster. (If the shader changes alone are responsible, then trying older versions could also help narrow down the specific cause.)
A somewhat unrelated observation: In a quick test, removing the folder with the modified shaders seemed to do no harm once the mod had been loaded. So it might be possible to write a launcher script for the mod that renames the original shader folder, moves the modified folder from the mod's dir to the BtS dir, launches BtS with the mod=... command, waits for a few seconds and then swaps the original shaders back in. I assume that the shaders actually get loaded before the mod, so, even if the mod's graphics take a little longer to load, that might be of no concern.
It would also be possible, I reckon, to distribute the mod as a standalone program – basically dumping the modified files into a copy of the BtS dir. An installer could create that copy from the user's local BtS installation to avoid copyright issues. But this is probably too laborious.
(And I don't mean to say that the current approach – shaders to be restored manually – is unworkable.)