I've seen this before. I've been doing RTI for about a year now. The T4 starts acting up a lil bit on me when the batteries are low. My suggestion is to leave the remote on the charger while the system is off, like overnight, and don't use the remote while its on the charger.

Overcharging the remote might cause some problems too. (when the remote is fully charged and on the base station, the voltage may be higher than operating voltage)

This will also damage the battery because while you're using the remote the voltage goes down (while current is being drawn from the battery) and it draws current from the charger. When its no longer drawing current from the battery to run a macro, etc, the voltage in the battery goes back up higher than the battery can handle, and it gets burned off with heat. The heat warms the lithium ion gel material and deforms it, thereby breaking down the electro-nuclear bonds and reducing the amount of charge the battery cells can hold.

I'm going into waaaay too much detail. The simple solution to avoid a problem:
Don't use the remote while its on the charger.

Side note: If the battery goes bad, you can get them extremely cheap from RTI distributors.