I'm using Cataloger, but in my template I also have an extra content block.

My layout is like this:

content | submenu
----------| second content block

However when I insert an Item page or Category page the information from this page is also shown in the second content block.

How can I fix this, besides using a seperate template for the Cataloger pages where I remove the second content block.

Sounds like you are using an old version of Cataloger as I thought this was fixed, it was one of the reasons I only tried it once as too many of my templates require more than one {content block}...

Please post system info...

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Extensions » Modules/Tags click the name of the module/tag or Help to the right to get its parameters.
Right click and view source is a great way to see what you have to work with.
Check ver. CMSMS, PHP, server OS, in System Information page.
Default content http://multiintech.com/defaultcontent/
Ever wonder what happened to the Album module? Well it is alive and well.
http://album.multiintech.com/

I'm using the latest version, but you are right it is a known bug:

http://dev.cmsmadesimple.org/bug/view/840