I assume you mean running chrome as a RemoteApp.
Are you using the --allow-no-sandbox-job as described here http://code.google.com/p/chromium/issues/detail?id=79091#c51?
Also there is a known issue with Flash that doesn't work with gpu acceleration turned on. So if you want to enable flash on that configuration you need to specify the --disable-gpu until this issue is resolved.
Now in case you don't run Chrome as a RemoteApp but rather run a full remote desktop session and Chrome crashes please describe when it crashes - immediately or after some time? You might want to switch metrics and error reporting in that case which will send crash reports to the developers and help them diagnose the issue.
As a general advice there - if you run all your session with the same user you will have to configure Chrome to use different profile directories for every session as described here: http://code.google.com/p/chromium/issues/detail?id=160676#c6 .
Last thing worth trying is to run the Canary version and check if it solves your issues because there are a lot of fixes that will come with the 24 and 25 versions of Chrome for that particular use case.