ugh... I have the same year and model of rig. I had this problem and found several causes:
1 - battery should be at best charger. A weak battery can cause this. Either connect to shore power (use the 12v converter or connect to the TV and use its battery.
2 - Fluid level. When the slides are in, the fluid level in the reservoir should be 1/2" from the top of the reservoir (I measured and marked this with a permanent marker so it's easy to see). Use the cheapest ATF fluid or acceptable alternative (ask if you don't know) that you can find.
3. Level and stabilized - The rig must be level and the jacks engaged to keep rig movement to a minimum. Apparently any unnecessary movement caused by the slides being extracted or retracted can cause undue stress and cause the motor work harder and get this problem.
Since we don't have the remote in a 2006 3500RL the most probably problem is:
4. Underrated CBs - If all the above looks good and you are getting this start/stop problem then the amps are exceeding the currently installed automatic resetting breaker and it shuts down the circuit waits a few seconds, then resets itself until it shuts down once again, causing the start and stop motion you describe. The CBs need to be upgraded. There are documents from the manufacturing stating that the auto resetting Circuit breakers should be rated between 80 and 100 amps. The factory often installs 40 or 50 amp CBs and this is where the problem can occur when the system is used with too many slides on the rig like our 3500RLs. The solution is to REMOVE the existing auto resetting circuit breaker and replace with a higher rated (or parallel combination) of circuit breakers. A single 100 amp, or single 80 amp, or dual 50 amp or dual 40 amp.
Per the instructions it is recommended you use new matching circuit breakers if you are using a dual set up (this is what I did) but it is more work because additional shunts are needed to construct a parallel circuit breaker solution (I could not locate discrete 80 or 100 amp auto resetting types). The new dual circuit breakers should be the same rating (both 40s or both 50s, not a 40 and a 50). It is not recommended to add to the existing one since the existing one is "old" and therefore should not be used with a fresh one. Or the easy replacement is to install a single 80 or 100amp breaker.
Here's the end result of my dual autoresetting breaker solution:
Note: the shunts don't have to be red or black, I just did it that way so I could spot the BAT side versus the AUX side. In my picture the red shunt is the BAT side.
If you need detailed instructions on how to do this, PM me and I'll email the specs and documentation.