That would explain the problem alright. I always used to install 4DOS, 4OS2, and 4NT in its own directory, but for Take Command I decided to use the default.
Actually, you can still accept the default selection. All my 4DOS/TCC batch files and script portions go in a custom directory like c:\batch. I install TCMD or TCCLE in the default directory under "C:\Program Files\JPSoft\". I also keep TCSTART.BTM there, and it has one command:
@c:\batch\tcc_newstart.btm
Note that it's not a "call" command, because I'm not going to return to "c:\Program Files\". The "tcc_newstart.btm" handles all the real initializations for me, which include rewriting the PATH, setting up 10 or 12 environment variables needed by my favorite utilities, loading my aliases from an external file, and changing the PROMPT to something colorful. (Oh, yeah .... In TCMD.INI, I do have ANSI set to Yes.)
So if you want, you can accept all the defaults, and still have full access to the TCC batch files and scripts. And when you upgrade, you can mindlessly accept the defaults, because the Install program will not overwrite TCMD.INI nor TCSTART.BTM.
HTH.