I also have stumbled upon that (or a similar variation in my poor jugdement).
You can also locate
pd.tk, anyhow it happend to me when the final tidying up (when compilling pd) was not fully executed, thus it complained about the location of pd-gui.tcl in my case.
pedro@io:~$ pd
Error in startup script: couldn't read file "/usr/lib/pd/tcl//pd-gui.tcl": no such file or directory
But this only happened when I started pd from anyplace. If I go into /usr/lib/pd-extended/bin
pedro@io:~$ cd /usr/lib/pd-extended/
pedro@io:/usr/lib/pd-extended$ cd bin
pedro@io:/usr/lib/pd-extended/bin$ ./pd
It loads correctly. Is this you case?