1. From a day of installation till the other day a lot of things could happen.
2. This piece of software is truly certain to be free of viruses.
According to the VT report (attached in the thread), all worth mentioned AV such as ESET, Kaspersky, BitOffender, and some others reliable did not flag anything..
Only a few questionable flagged something and none of them said anything close to rootkit as you claim.
So ask yourself where did you go meanwhile and what did you do there?
Virustotal (again):
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In VM just for this purposes:
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Also with Process Explorer, I observe what will happen when I run the key generator. Of course, nothing to report.
EDIT: Alos more than hundred downloads.