And even when you fix the ACPI, DMA interrupts have priority and can still interfere with Mach3 operation.
Is it using Virtual ACPI. Timing latency now can be an issue.
Do you have file indexing on? Disk drive light blinks a lot?
IDE drives, can cause problems. Include DC/DVD even when not being used.
Can you try a SCSI drive?
Some things explained. If nothing, read the last paragraph.
Time
Super X3. 3600rpm. Sheridan 6"x24" Lathe + more. Three ways to fix things: The right way, the other way, and maybe your way, which is possibly a faster wrong way.