Can applications mess up the ROM?

[New Daddy]

I've had the following symptom happen to my first XV6700 and now to my replacement XV6700:

Occasionally, its screen fades away and turns white (not black) and freezes.
When this happens, sometimes soft-reset succeeds in waking up the phone, but usually the phone just stalls upon the "Windows Mobile" welcome screen, requiring 6-10 soft resets.
At worst, I have to hard reset the phone, because soft-reset just wouldn't wake up the phone.
Even after a hard-reset, with no applications reinstalled, this symptom would recur.


The customer service representative at Verizon that handled my case told me that sometimes applications fry the system that even a factory-reset can't cure the problem.
So my question is, is that true?
I never hacked my ROM. Regardless, can some applications fry the ROM?
All the applications that I use are popular apps - Spb Backup, Spb phone suite, Agenda Fusion, SK Tools, etc.
Are these types of apps capable of wreaking havoc with the system?