Had a problem with a stock fan a couple years back where it would spin up really high for like 10minutes then it would go really slow for 30minutes then sometimes it would stop completely for 5 seconds and then spin up again. If this is similar to the same problem then I would just replace the heatsink and fan on the CPU. If it is actually the mobo fan and not the CPU fan then I would try a new fan. Older fans had a tendency to fail alot more frequently than they should.