Sounds like something is horribly wrong with the installation, sufficiently badly that if it was widespread it would've already been picked up on. Thus it's probably a problem with the R installation (or how Tcl/Tk are packaged within it) and so you should ask with those guys first.

The infinite-loop errors are probably due to everything going through the unknown command handler over and over. The missing close-bracket is just mysterious. You should be prepared to tell whoever you report this to next what the contents of those pkgIndex.tcl files are (they shouldn't contain anything confidential).