Can you describe the alarm, is it a constant beeeeeeep, or a high-low-high-low siren, or a monotone beep-beep-beep? You mention heat sink, is that a passive heat sink (rather than an active tower cooler)? Those are designed for server chassis with very high airflow from a bank of 40mm high-rpm fans. Your CPU might simply be overheating.
One upgrade path to consider is NK4.0. There are mATX options that fit your case, e.g., X9SCM/SCL. The downside is you will have to get new RAM, assuming you currently have RDIMM – socket 1155 requires either ECC UDIMM (e.g., 10600E) or non-ECC UDIMM (e.g., 10600U), depending on the board. UDIMM is not as cheap as RDIMM, unfortunately.