ISAPI filter and App-Domain error

I have an odd error with an ISAPI filter.
I have a complex web application installed on IIS 6.0 on W2K3 SP1. The web
site uses a mix of NET 1.1 and 2.0. Each component operates a separate
virtual directory, and its own application pool. This has worked fine for a
long time.
I had to reinstall one of the application components. Since then I have had
two errors:
- A DCOM error that the network service is unable to run a CLSID that
appears to be MSIServer. I also have a windows installer error saying 1015
error failed to connect to server. I am assuming this is one single error. I
don't know why the network service (the app id) would be trying to run or
repair an installation, but I guess it has something to do with the NET
framework
- My NET 2.0 components all fail with a browser error, server unavailable,
and on the web server an error 1088 Failed to execute request because the
App-Domain could not be created. This error goes if I downgrade the
components to run as NET 1.1, but then of course the code can't execute.

The curious thing is that the web application (which runs as NET 1.1) has an
ISAPI filter running on the site. If I remove the filter, error no.2 goes
away and the site functions normally. Error no.1 remains, but does not
appear to affect the functioning of the site.

So re-installing an existing components seems to cause two new errors; and
an ISAPI filter that has previously existed seems to cause the NET 2.0
components to fail entirely.

I have re-installed both NET frameworks but that does not help.

Any ideas what the problem could be or how to fix it?

Thanks,
Anthony