i was using 4 fans, all well suited ... i found this out tinkering w/ the bios and makings some settings to just let the fans run at full speed and ignore the temp ... it did run like an airplane, even w/ the side cover removed. i'm still puzzled as to how dust can accumulate inside the tower. if i was smoking in the house or had pets, i could see this as probable.
i guess my previous advice obviously didn't help, which leaves me wondering if perhaps your motherboard bios settings might be misconfigured, as primarily the cpu fan is controlled from here. you stated you are within a tolerable range for your cpu range ... and also am assuming your testing that with a in-OS 3rd party software. have you compared that temp to what the bios settings are set for? i guess ya' could reset the bios, take notes on the max ... it should be properly rated if you're using a standard cpu for your mobo. i think i would definitely look up a suitable range for the cpu and manually set that in the bios.
anywho, the last thing i want to do is leave ya' w/ advice that might over-heat the cpu. you do have the fans plugged into their proper places, cpu - on-board mobo cpu fan, chassis fan ... i always ignore this setup opting to move a fan w/ the greatest throughput to the inside of the PC or as close as i can to the memory cards, gfx, or hard drives ... i guess as a final note, have ya' actually isolated the fan that's running at full speed for this period: cpu, chassis, i have an extra one on mobo, gfx ... ?