I'm in the same boat. Ironically I had it working at one point but as part of spring cleaning I've done a clean install of Windows and Adobe CS5.5 Master Collection and all went well except installing FB 4.6. It wouldn't recognized the serial number OR allow me to install on anything but the C drive. I have an SSD drive for Windows and all my apps are on an E drive.
Originally I had CS 5.0 Master Collection, installed the 4.6 trial, I then upgraded to CS5.5 and as soon as I installed the first app (Flash CS5.5 Professional) with the CS5.5 serial, FB 4.6 came along for the ride and it was no longer a trial version.
Hmmmm. So yeah, I would like an answer too. I'm currently on hold
FB 4.5 and FB 4.6 can't co-exist on same system. So we need to uninstall FB 4.5 and iOS Component(which is installed as a part CS 5.5) and then install FB 4.6. Please follow the steps given at http://helpx.adobe.com/flash-builder/kb/flash-builder-4-6-doesnt.html.
Also install FB 4.6 in trial mode.DON'T ENTER SERIAL NUMBER AT THE INSTALLATION TIME. After that launch FB 4.6 and in the trial screen enter the CS 5.5 serial number.FB will get serialize.
in another thread jleydig has mentioned very precisely how to serialize FB 4.6. Please follow it for serializing FB 4.6
1) Deactivated CS 5.5 by going into Flash Builder clicking Help > Deactivate Flash Builder...and clicking "Deactivate Permanently" (which deactivated the entire suite)
2) Uninstalled only Flash Builder 4.5 and the iOS Component through the Control Panel (I'm sure you know how to do but just in case... go to Control Panel > Programs and Features (terminology may vary based on your OS) and click on your CS and click Uninstall. This will launch the Adobe uninstaller. From there deselect everything and only select (check) Flash Builder 4.5 and the iOS Component and then uninstall them - uninstalling the iOS Component might not be necessary, but I did it anyway)
3) Restarted after those uninstalled
4) Launched Photoshop and entered my CS Serial Number (you should be able to launch any CS program thats still installed to do this)
5) Once it opened, closed it
6) Installed Flash Builder 4.6 in Trial Mode making sure to select the same language used when CS was installed (that's IMPORTANT)
7) Launched Flash Builder 4.6 in 60-Day (or however many days it was) Trail Mode
8) Once it opened, closed it
9) Launched Flash Builder 4.6 again, but this time I entered the Serial Number from my CS (at that point it accepted the SN and opened like normal and has everytime since)
10) I then installed my iOS Component from my original CS