No. After activation mods in JSGME just shut down this soft.
And the most important thing is... What mods are you trying to enable? I`m almost sure you are talking about this one:
NewUIs_TDC_6_9_0_ByTheDarkWraith - this is zip archive. Unpack somewhere else and look into this folder. There are a lot of different mods inside.
For example:
D:\Games\SH5 MODS\NewUIs_TDC_6_9_0_ByTheDarkWraith and there are MODS, Documents, and Dials.
http://www.subsim.com/radioroom/albu...pictureid=5632
Some archives have such a structure. So look inside before.