With the exception of Rockwell and Siemens, who together have maybe 70% of the PLC market, most PLC programming software has a tiny user base when compared to software for the general public. It would be hard to get actual numbers, but there might be at most 10,000 users of Omron's programming software world wide world, while there are well over 1 billion users of AVG anti-virus, to put things in perspective.
Software with such small user bases will always have disproportionately more bugs and respond slower to changes in how Windows works. For instance, Vista, 7 and 8 all have special protections on the 'Program Files' folders that are very different from XP, so any PLC software that was originally made for XP should not be installed into Program Files folder to avoid many mystery problems.
Generally, Windows Updates will have no effect on most software, but some PLC programming software tries to do weird stuff to verify you've paid for it or communicate over a proprietary protocol to the PLC. These things can be effected by some security updates and if the software is older, there will not be an update to fix the issue (current software will be updated and will have information on temporary work arounds). You should keep an old XP laptop with a real serial port if you rely on outdated software.