Do you gave a gain knob on that amp? If you have a SensarPro in-line anywhere, set it at 10 or below and see that that does. If you're not touching anything I think (from 3000mi away)that you might be getting whacked by a much stronger carrier nearby. These amps are fairly straight forward, often having only one transistor with lots of frequency select tuned circuits surrounding the one device. The point of all that is to pass the TV bands (usually including FM, but there may be a switch) and filtering all else out for possibly this reason.
FM licensees OFTEN have more than one transmit site that they locate their backup transmitter(s) incase of catastrophic failure at the primary, and they use them regularly. A little 5-10KW backup transmitter will fit prettymuch anywhere. Its possible you have a primary or backup causing these intermittent problems.
If this VHF is as strong as you say, try unplugging the amp closest to the antenna and see what that does