Yeah, I suppose that could happen. I also don't have a low-pass filter on my sub. I usually set my sub/main integration using RoomEQWizard, so they're usually pretty close. I also use the meter to verify, but I don't recall having such a disparity between the sub "tone" and normal playing.
I suppose it's also possible that the sub is exciting a particular frequency, and that the SPL meter is picking up on that small band of high energy. These SPL meters are pretty coarse, and will generally return the value of the hottest band that's being measured. If you don't know the frequency response of the sub, it would be hard to tell.
Have you ever used REW and/or parametric equalization on your sub? If not, you should check us out in the "REW | BFD" forum of "The Home Theater Shack". Those tools open a new universe for sub clarity. The Velodyne SMS-1 is another popular option as well for parametric EQ.
Anyway, at this point, you may just have to set your sub by ear, at least to some degree. Even when things are set up right, I have to tweak by ear based on the program material -- some recordings are just too thin in bass, and some too heavy.
Good luck!