Yes, I have a ton of mods, unfortunately.. I primarily have IFS, but think some mod might have dragged in others too. I also have RemoteTech, and I have tried switching between the space center and back, load and saves, and it still messes it up. I do have enough resources available also. It mostly seems to be with Liquid Fuel or Oxidizer, Monoprop has never failed to transfer thus far.
I noticed another problem with RemoteTech, as I built a probe I forgot to put an antenna on, so I did an EVA and moved an antenna from a docked craft to the unreleased craft before releasing it. That did cause some issues with RemoteTech but it vanished after "buildtime" amount of time had passed.. But that problem I suspect lies more with RemoteTech...