We use Wix to create our MSI installer. We have a few custom actions that work great when using the installer normally with a GUI, but when using silent install (with "msiexec /qb /i" ), the custom actions won't run.
What can I do to make them work through Wix?
I suggest you read (several times if needed... it took me awhile at first):
Installation Phases and In-Script Execution Options for Custom Actions in Windows Installer
There are a great many things to consider when authoring questions and the details are in that well written article. Basically it sounds like you only put the custom action in the UI sequence and not the Execute Sequence but there are other things beyond that you should make sure you are doing correctly.