All things are possible but I don't think deleting the GSAK install is the issue here. If it were a damaged program file or an overwrite of a DLL (as we've seen with Chilkat) then just doing a reinstall would fix it without needing to delete the old.
Instead I suspect that something odd might be happening in the GSAK Temp folder (as mentioned above but with an incorrect path). It could be lingering old data, or a virtual store issue or something else ??? caused by a change in Windows. (The one thing we do know is that it's not a change in GSAK)
I've never seen the problem but, if you are one of the unlucky sufferers, then please try first closing down GSAK normally, then deleting the GSAK Temp folder which, in a normal install, will be at C:/Users/YourName/AppData/Roaming/gsak/Temp. When you restart GSAK this folder will be re-created.
GSAK uses the Temp folder as the temporary store for downloaded PQ zip files, and unzips them to a zip folder in there. By deleting the Temp folder we are clearing out any lingering old files. I'm wondering if a permission issue or Windows file protection of some kind, like the Virtual Store, is stopping the unzip process from overwriting older gpx files from the same PQ - just a guess as we have no hard evidence.
Either way, if this does or doesn't work, please let us know.
(Though I did have my fingers crossed when I activated the api. 
)
Happy to help.