This problem is often indicative of a commerce context initialization problem, or an environment where you are hosting many CommerceServer Sites on a single machine.  This can happen because each CommerceServer Site has many perf counters for each of the various resources (catalog, orders etc) and these counters multiplied by multiple sites can exceed the default size of shared memory for these counters. Good news is that this default size can be increased. See MSDN.  But it’s probably not a bad idea to put some tracing around your context initialization code to insure that there aren’t multiple or un-necessary context creation calls.

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The Catalog Manager app uses the web service to do the import, so I would guess that you haven't properly onfigured the permissions.

Check that the identity of the App Pool that's using the Catalog Web Service has write access to the following:
1) The CatalogAuthorizationStore.xml file in the catalog web service folder under IIS
2) The Windows\Temp folder
3) The Temporary ASP.NET Files folder under C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727

Also:

1) Open the Commerce Server 2007 command line prompt
2) Type csconfig.exe /r Feature.MS.CS.PerfCounters

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