Problem with Honeywell RTH 6300B T-stat

I purchased this t-stat last winter:
http://brigita.blogspot.com/img/Therm.jpg
It worked good for my heating system. But I recently turned on my CAC for the first time and noticed a wierd problem. The T-stat has a built in compressor protection feature. It waits 5 minutes before starting the compressor if the T-stat cycles too quickly. Which is fine only theres one problem: When I tested it out, the compressor came back on, but the blower motor stopped working, as if the 2 had been reversed. I double checked the T-Stat wiring and it is good. According to my Trane furnace schematic, the compressor relay is hooked up to y and c terminals on the furnace circuit board, which they are. A point to note, there is no C terminal on this T-stat. The manual says " Do not connect the c wire, you will not use it". Also there is an R and RC terminal on the T-stat jumped together. The manual says to leave the jumper connected if all I have is an R terminal on the furnace. I plan to call Honeywell for support, but does anyone have any input what might be wrong?
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Mikepier wrote:

Maybe the high speed winding on your blower motor is faulty or disconnected? Does the blower motor run if you set it to "on" rather than "auto" at the thermostat?
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The fan switch functions normally. I believe that my fan motor is only one speed. Although there are 4 leads coming out of it, I think its configured for the highest speed.
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UPDATE: Well, I don't know what happened. I tries it again this morning and it seems to work. Both the blower and the compressor does not come on now. I'll keep an eye on it. But I could have sworn that was not the case yesterday.
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