I found this is a Thermal warning beep code on page 81 of this: http://downloadmirror.intel.com/15141/eng/D945PLNM_TechProdSpec.pdf
What can I do to be sure my heatsink is touching? can the pc really be overheating if it hasnt been running?
In fact, that beep pattern is related to over heating issues.
Please bear in mind that this product has reached its End of Interactive Support so Intel no longer provides interactive support for this product via telephone, chat or e-mail.
What you may do to test this, is to test the system out of the chassis, placed on a non-conductive surface like a newspaper, a magazine or something similar, and testing only with motherboard, power supply and processor, Heat Sink/fan, one stick of memory and the video card.
Then clear the CMOS removing the CMOS battery and all power cables from the power supply to the motherboard, leaving the system without power for 20 minutes at least, then reconnect the power supply and place back the cmos battery and power on the motherboard.
If it works that way, try adding devices one at a time.
One thing I would like to check is, what is the model of the processor installed in that system?