I have run into that problem before.
And Francois has also, even if he does not realize it.

I now try to do a:
   ./configure --prefix ...; make distclean; ./configure --prefix ...
every time.
I agree, the build system is quite sucky.

Given --prefix mypath, tk configure should look in
first.   And if --with-tcl is specified, it should look there first.
Not in random other places.