Turns out that Viral Matrix is exploiting a loophole in the way that individual effects are applied by a periodic ability of this nature, which prevented it from being cleansed using conventional methods. You see, the effects don't have a duration until they are active. So while VM has 3 shut-down cycles, only one is ever active at a time and they are 4 seconds apart from one another. And since EngTeam only lasts 5 seconds, the best you could ever do is prevent 2 of those cycles from occurring, and the third would become active outside that safety window.
We've just managed to prototype and implement a new method for cleansing debuffs of this nature, which we haven't made use of on STO in the past. After this fix is patched in, Engineering Team will finally be a true cure for Viral Matrix (as well as the version caused by the "Viral Spread" Doff).
this is exactly what i have been experiencing! glad its not that im crazy, thats exactly whats been going on.