Im assuming that you have set the minimum value of the supply ships correctly. How much time did you wait for the MSP to be transferred when you decided it wasn't working?
I had a similar problem with tankers and fuel until I realized that I need to wait hours not minutes of game time.
Additionally, resupply from supply ships probably didnt work because both the base and the ships are considered supply vessels, ergo they will supply the rest of the fleet but not eachother since they are all above their minimum supply. This might be annoying micro but try to set the base design to be not a supply ship and see if the problem persists. Once it is filled up and the supply ships have left you can redesignate the base as a supply ship. (you dont need to unlock the design to mess around with designations like tanker, collier and supply). You could also try to set the minimum supply of the base to 100% MSP and then move it back once the supply is done.
Minimum fuel and supply was set to zero on the base.
10% fuel, zero supply for the ships.
I hit 30 day increment after issuing the orders, game stopped and gave me the message than the fleet had completed its order to resupply the base after a few seconds. When I reissue the orders, sometimes it stops after 5 seconds, sometimes it takes 2 minutes, sometimes 6 hours.
Just tried unticking the "supply ship" option for the base design and played with the minimum supplies, the ships still won't top off its MSP when ordered, neither with the "resupply from own supply ships" order, nor with the "join & resupply target fleet" order.
However, if I:
Untick the the supply ship box on the base design
Merge the resupply base with the resupply ships
Have the resupply ships set to "resupply own fleet"
Wait
The supply ships will slowly fill the base's MSP. Unfortunately this is an unacceptable amount for micromanagement for something that should be trivial, and I don't know how to automate it. I'm now trying to figure out a better way to maintain defense satellites indefinitely at a jump point.