First of all, Adobe Flash Player (from here) has never had malware of any kind in it. Adobe isn't in the business of distributing viruses and they never have been.
There are literally thousands of "rogue" sites out there that have an "official look" to them and the are offering all sorts of infected ware, under the name Flash Player. Unfortunately Adobe can't keep up with all of them and since Adobe doesn't run the whole internet, they can't stop them or shut them down without going through lengthy legal proceedings, since most of the offending sites are outside U.S. jurisdiction.
The latest release (2/4/2014) WASN'T because the previous version "contained malware". It was released to fix identified security issues. There's a new virus or derivitive of a known virus created for Windows every 20 (twenty) minutes. Adobe normally releases "incremental" updates every six weeks, but when a new vulnerability is identified, a "security patch" like 120.0.044 is released ahead of schedule. That doesn't mean it "contained malware" by any stretch of the imagination.
If you have malware, you need to get rid of it, using your Anti-virus.
If your Antivirus has "out of date" definitions, it'll give you a false positive on clean files. I've seen it hundreds of times in the last year. Some A/V software is abominable when it comes to keeping up, quarantining Window updates even.
The REAL Flash Player downloads are here:
Anything else, from anywhere else... is a fake.