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I'm afraid I can't weigh in on your particulars but it's worth noting that it's very common for today's PCs to share IRQs between multiple devices successfully.
You'd lose your middle-button functionality, of course, but have you considered switching to generic mouse drivers to test?
One of the most frequent problems with Windows machines is poorly written hardware drivers. Because of the driver software's role in the system, a badly written driver can affect other apps or processes seemingly completely unrelated.
That's the reason everyone always says: make sure your drivers are up to date. Sometimes, being up to date is not enough. Drivers are exensive to develop and test and some makers/repackagers are less than thorough in that dev/testing.
Driver stability was, in fact, one of the primary reasons MS put such an enormous testing and certification emphasis on drivers under XP and later OS versions. (You know that nasty little warning screen that Windows pops up when an uncertified driver tries to install? MS was tired of getting blamed for bad third party drivers so instituted a bunch of high hurdles for testing, etc. Ignore that warning at your own risk. [But sometimes you gotta if you want to use a piece of hardware (like my old Echo Mia) whose manufacturer didn't/couldn't go through the expensive and timely testing/cert process.])
Anyhow, since it's a "third mouse button" that's triggering the issue, I'm thinking the mouse driver is the first place to investigate...
Good luck!
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