My best guess from reading it this.
2 subs (4 ohms each) wired with both positives and both negatives together will get you a 2 ohm load on the amp. Now, if your amp is 2 ohm stable (fairly common), it will run fine with a 2 ohm load, but it will go into safe mode when anything less than a 2 ohm load is applied.
Now with 3 - 4 ohm subs wired with all positives together and all negatives together will yield a 4/3 or 1.3333 ohm load, which is less than 2 which would cause the amp to go into safe mode.
Try this, unhook one sub and only run 2. (run positive wires together and negatives together) If it runs fine, the 3rd sub is dropping the ohm load too much.
If 2 work, you would have to either purchase a 1 ohm stable amp, or wire the subs differently...and the only other way to wire them so they all get the same power would be to wire them all in series. This would result in a 12 ohm load. You would not want this, running 2 of the subs would be better.