Just upgraded to KSP 1.4 on Mac / Steam [new to forums so if logs are useful, please point me]:
I am getting the same issues. On a save game (Science mode) where I have unlocked the whole Stock tree, a craft that used to have TCA installed and working [all modules] now appears to have TCA in the SPH, and when launching, the TCA icon is present, TCA can be enabled/disabled using standard key Y [icon grey to green etc] but clicking the icon does not show the usual grabby windows for controlling TCA functions. I've tried a full reinstall of TCA (3.5), Module Manager, and Aquila Enterprises (bundled w/ TCA).