Causes and possibilities may include but are not limited to:

Alternator; Mags; Strobe lights; Bad capacitor at the alternator; Bad ignition leads at the mag/sparkplugs; Bad ground plane at the antenna, bad antenna, bad ground plane at the radio rack, bad ground crimp, bad autopilot servo, bad servo relay; bad beacon light; poorly grounded beacon light; and a whole host of other things. 

Usually, something is not grounded or shielded well,  or something is inducing enough noise in line to bring the threshold high enough that very little "extra" is pushing it past the squelch point.

It is important to remember that the IFD is a digital radio, analog radios are not as easily affected by electrical noise and therefore an analog radio in the same position will not isolate the problem. The best way to isolate a digital radio from being the root cause is to introduce another digital radio in it's place, preferably an IFD, as others tend to have different sensitivity threshold. 

The easiest way to troubleshoot this type of issue is to make it fail, then start pulling breakers in the aircraft one at a time, and test the VHF each time.  When the breaker is pulled that finally allows the unit to function correctly, you have very likely found the circuit causing problems. Once you have the circuit nailed down, finding the actual root cause is often a tedious process. A bad crimp, for instance, will ring ok with a meter checking continuity, but can induce noise when it has actual current flowing through it.