Well...you mention three variables which, IMO, could possibly account for any system problem.
a. Acer. I'm not being mean, but I have never thought that buying a system from any OEM manufacturer (Acer, HP, eMachines, etc.) where they install and do things their way...is one more possibly complicating factor that can be avoided by building my own systems. I'm not a laptop lover, so I can have my attitude and do straight installs of Windows without considering reoovery/restore mechanisms, atypical boot scenarios, and hidden partitions.
b. Malware...no need to elaborate on this, other than to say that (IMO) many persons who attempt to self-heal systems they have allowed to get infected...may not necessarily be very astute at recognizing and removing infections.
c. Hardware issues. Hard to troubleshoot without a methodical approach, IMO.
If you truly have resolved your system issues...a tip of the hat to you and thanks for posting...it may help someone out there and that's what many of us try to do, within the realm of what we know and what we choose to learn.
<<Could a trojan go into my partition and change my recovery password?>>
I am not smart enough about malware to answer that
, but I will say that files become damaged every day...both as the result of malware and just in the process of normal computing. Since you've cited a known malware situation...I'd be tempted to blame it, whether it was a direct result or an indirect one...but that's just a very uneducated, simple approach I take with such situations.