I wish you had made it much simpler, in terms of actually how to use the mods people download on here. It can not be expected of everyone to understand these terms, as I certainly do not. I don't understand what $INT$ is, even from a google search, and I certainly did not see this alleged folder anywhere in any of the versions I downloaded. I could not use a single mod I downloaded, after spending about 2 hours looking for how to do it. The guides are of no help and neither are some of the replies. I am giving my rating because, while it may be a good loader, It is terrible in terms of user-friendliness so much so that I do not plan on touching it until I see a reply that gives a clear answer as to how to use the mods present within this community.
I don't think I've had that exact issue, so I can't give you an exact solution. But you could try changing the order of the mods in Mods.txt or renaming the mod(s) to one of the following names: "Char.swf", "Mod.mod" or "Mod.swf". (since they all(?) get loaded when a character folder is loaded if my memory serves me right)
Loading mods has always been error prone in my experience (even before I started working on SDTL) and I've had quite a few problems/bugs related to it while developing SDTL and my other mods. But I would like to solve this issue, so please send me a PM with more details about your character folder & what mods are listed in your "Mods/$INIT$/Mods.txt" file! : )