Gerrytan, you are using bash syntax on a system that does not use bash syntax.
Specifically, when you do the following:
echo 'junk.txt' >> .gitignore
You have told git to ignore the file 'junk.txt' including the quotation marks.
If you had used bash, or any sh-compatible shell, then that command would have told git to ignore 'junk.txt' excluding the quotation marks, because in those shells, the quotation marks indicate the word boundaries, but they have no special meaning in cmd.exe (The standard command line in windows).
I suggest you open .gitignore in an editor and take a look at the entry.