With the software upgrade, I've found that it's now necessary to use two HTML tags to get proper white space behavior, both <pre> and <kbd>. The former allows multiple space chars to be preserved, while the latter is needed to force the use of a fixed size font. Also, the <kbd> tag needs to follow the <pre> tag, as illustrated below:
Some descriptive text, blah, blah, blah
source code or CHARMM input script
Don't forget to select "Using HTML and UBBCode"