If you go with Windows systems you will be redeveloping the software often and it will be running on a unreliable platform for that application.
However if the system isn't Critical and down time isn't an issue then by all means go with Windows though which ever way you go it will limit the possible sales.
But M$ has a habit of with every new release of Windows the software that runs on it needs to be rewritten so the users have one of 2 options wait for a Rewrite of their Critical Software or stick with what they already have. Many times software is not rewritten for new versions of Windows because the costs are just too great to justify a rewrite for the limited market that, that software services so it remains the same and eventually gets dropped as a Salable Product and is given away so that existing or new Hardware can continue to be used and sold. There are many Specialist Applications like that which where a leader in their field once and the companies who wrote them have dropped them in favor of proceeding down a different path of they have gone out of business for whatever reason these applications and the hardware that goes with them become obsolete and the people who use it can not replace it with current generation software/Hardware combinations so they continue to use what worked the best for them and the Hardware gets older and older costing more & more to support.
I have a couple of Specialist NT Applications that simply do not run on anything newer than NT4 and I have to keep those systems running. Similarly I have a couple of clients who use a DOS App and finding new hardware suitable for those computers to replace the old ones when they die is getting harder and harder to come up with but it has to be done to keep the production floor running.
Personally I would Port to Linux/Unix and go with that option it is just easier and for Long Term use makes a lot more sense.
Col