On my 124, there is a lateral shaft (side to side) with a gear on the left end underneath the takeup spool. The gear (and therefore the shaft) is turned by the rotating film on the takeup spool. I believe - but am not certain - that this shaft operates the film counter. Because it's operated by the film it's, in effect, measuring distance along the length of the film and is therefore not impacted by diameter of the film on the takeup spool.
If I'm right on this, the issue could be with lack of contact between this gear and the film. Not likely (more likely an issue internal to the wind mechanism) but worth a look.
Regarding the $85 CLA, what does that include? My guess is that it is for a CLA of the lens/shutter and won't address your issue. So verify. If $130 ($85 + 45) gets you a properly serviced and functioning TLR, you're still OK.
But based on a estimate for a 124G I got a few years back, Mark Hama charges something around $175 (going from memory, so don't quote me on this) for a CLA. However he goes through the entire camera and provides a warranty. He probably does charge a premium, but I'd say most of the difference is due to the scope of work.
Alternatively, you might try reselling it as a parts/repair camera. There are a few "repair hobbyists" out there will to pay $20-40 for the camera. You can try here on apug or on the Favorite Classics repair forum (http://www.kyphoto.com/cgi-bin/forum/discus.cgi). You might even find DIY instructions there.