The VC5090 will only cope with running the IE (Internet Explorer) engine. To install into the Application folder run the Enterprise Browser desktop installer and select "Enterprise Browser - IE (Persistent)" under the 'Windows CE' options.
Once the .cab file is deployed and installed you should see an Enterprise Browser folder structure somewhere under \Application.
To complete installation, you'll need to cold boot the device. Given the error message you describe I suspect that's the missing step. You can find instructions to cold boot in the device integration guide from support.symbol.com (https://atgsupportcentral.motorolasolutions.com/content/emb/docs/manuals/7634606a.pdf )
Whilst Enterprise Browser will work in the technical sense I would advise against using it for developing new applications on the device. Exactly which APIs are and aren't supported with the IE engine isn't explicitly documented, the primary design here is to support older applications written for PocketBrowser