The custom action may fail to run because of the assembly schema specifics (e.g. method names or presence of other entry points).
In the attached file you can find the example when perfectly working MSI with managed CA can be broken simply because some extra method added to the managed assembly with custom actions.
Tested against WIX (Windows Installer Xml) version 3.0.4805.0
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Sample contains readme.txt with the problem details
Please try the final build of WiX3.0 (5419.0).
This Tracker item was closed automatically by the system. It was
previously set to a Pending status, and the original submitter
did not respond within 14 days (the time period specified by
the administrator of this Tracker).