That's a brand new problem, which is a sign of either tapping the plus key without knowing it (easy enough to check out) or a corrupted file somewhere. Just to set your mind at ease, I'd recommend a complete reinstall. You can do it without losing any custom settings or save games.
First, just move your mods directory to your desktop for safe keeping. Then uninstall SH4 using Add/Remove Programs. You will get an option to save all save game data. Do it.
Now, reinstall SH4 and patch 1.4 from scratch. Install JSGME and run it once to make an empty mods directory. Copy all the mods from your desktop mods directory into the new mods directory in the SH4 folder. Delete the desktop mods directory. Reinstall all the mods with JSGME. Play as if nothing had ever changed, except hopefully your problem will be gone.
If I left anything out, somebody please correct me!
