I can't reproduce this problem.
What I tried:
- Made a custom series column hierarchical using preferences -> look & feel -> tag browser
then:
- edit a book with no value in the column. No problem.
- edit a book with a value in the column. No problem.
- change a value in the column to contain a period. No problem.
Is there any chance that you changed the lookup name of an existing custom column to one that existed sometime in the past? That can create difficulties.