The quick answer is no - there are not any Windows x86 programs that will not run on AMD processors. There may be some very weird, very proprietary and strange flukes, but there should not be any modern x86 programs that do not run on AMD CPUs.
In the Win95 days, there were some programs that would not run on AMD CPUs. A good example was (I can't remember the name!) a racing game made specifically for the Pentium 54C P90, 100, and 133 CPU's w/MMX from Intel. I can't remember the name still, but that game would not run on a 486DX4, PII, or P3 machines. It simply would not.
In my experience, the list of apps that are not compatible with AMD CPUs is limited, and very limited at that. The best option? Contact the publisher of the software program, and made them aware of the issue. AMD CPU's may not perform as well as Intel CPUs do to compiler or architectural/performance metrics, but should run almost all x86 programs nonetheless.
Moving to the next step, it is also unlikely but much more possible that yes, the AMD/ATI SATA or AHCI drive controller drivers are causing a compatibility issue with the software you're running. This is really a software issue with the program rather than the driver, since it is and would be ridiculous for a software company to exclude disk controllers besides Intel.
First step - If you're running a board with an AMD/ATI chipset (ATI6xx series or AMD 8xxx or 7xx series) chipset, update the drivers. Drivers are available at AMD's website.
If a driver update does not work, contact the software publisher/programmer. They may have a fix or be able to helpe further.
Hope this helps!