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16 bit application no longer runs with hyper threading

We have a 16 bit application that has been running fine on WIndows 2K/XP, until the hyperthreading technology was introduced. Now when the the application runs, it locks up the entire machine, to where the only way to stop it is to turn the machine off.
The program uses the serial port for comminication toexternal devices (microcontrollers).
I havecreated an application that will only run in one processor (SetProcessAffinityMask) to spawn the 16 bit application, but that does not work either. The software has evolved over the last 10 years, and we are not in a position to re-write it entirely.
When I go into the bios and disable hyperthreading, it seems to work better, but some machines, laptops in particular, do not have the ability to disable hyperthreading.
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Honored Contributor III
The Windows 98 compatibility tab option of XP 32-bit seems a simpler way of restricting the application to a single logical CPU. Does it give the same results?
Microsoft has been warning about phasing out 16-bit support for over a year now. The latest versions don't have any 16-bit support.
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