Homebrew PCBs

> yet the gerber when sent out to a board house created some real headaches.

The board house does not use the gerber file to drill your boards. In the
package, I suspect you sent them an excellon or NC drill file. This file can
be opened with a text editor like notepad and can be edited if it is not
correct. One would need to have an understanding of the excellon output to
do this.
-Mike