I have tried several attempts to have an SSI command inserted using the category template in 2.0. The command works fine for one directory level like categories. The SSI command must be referenced like ../../cgi-bin/program.pl and will not work using http://www.site.com/cgi-bin/program.pl. Because of this, if the SSI works in one directory level it won't work in another level like subcategories because the ../../'s don't correspond correctly. Any suggestions?

Can you show the specific SSI command? It is hard to know what to answer without knowing what you are trying to do. There are many SSI and Extended SSI commands available.

Sorry, I am trying to execute a perl program. The command is
<!--#exec cgi="../../../cgi-bin/directory/program.pl"-->

Thanks

all you need is
<!--#exec cgi="/cgi-bin/directory/program.pl" -->

when using ssi calls all you need is /cgi-bin/directory/program.pl..i use ssi calls all the time and they work fine without the:
../../../cgi-bin/directory/program.pl

bye for now.

I tried to add SSI calls to my generated pages and they dont seem to work. For example I have <--#exec cgi=/cgi-bin/Bannermaster/bm.cgi" --> added to all the all my pages (templates) and they dont seem to work. Any suggestions?

maybe it's because you have:
<--#exec cgi=/cgi-bin/Bannermaster/bm.cgi" -->

and NOT

<!--#exec cgi="/cgi-bin/Bannermaster/bm.cgi" -->

hope that helps