I use them for all my videos when available and I have never had any problem. Make sure the filenames are identical and only the extensions are different. VLC is more forgiving in that respect so maybe thats your problem.
Figured it out it was user error…i kept the settings from my original set up 1.0.4…even when i swapped before i still kept it….deleted the settings loaded wiimc 1.0.6 and subs .srt work perfect.