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@vinieux- there have been problems with K//aspersky from time to time. It would be better if you did a a search of the Calibre forum for Kaspersky and reached your own conclusions. Many of the AV packages and security suites have caused problems at some time or other - have you tried accessing your portable in Safe Mode with no internet and Kaspersky disabled (if it permits) and/or exclude the calibre portable folder on G: from Kaspersky's processing.
Also have a look at the FAQ Miscellaneous section in the calibre user manual, it documents a number of 3rd party products that have been known to cause problems - not always for everyone who uses them - Wacom devices and SpiderOak are a couple that spring to mind.
BTW did you use the Free version of Geek Uninstaller or the Pro version, latter claims to do a deeper scan, no idea if that's so. Could be that it only does that if it monitored the actual install when it would create an transaction log to use to rollback changes when doing the uninstall. That's how some other Pro Uninstallers work - like Revo and IOBit.
BR
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