Run the inventory scanner with these additional switches. /f /sync /o=c:\outputfile.scn.
This will cause a full inventory scan to be ran and also dump the client side inventory scan to c:\output.scn prior to send the scan to the core. You can open that scn file with a text editor and see if the data is in there.
My initial guess is either the /f /sync will send the data you are missing as you are now doing a full scan or you have a syntax issue in the ldappl3.ini. If it is the later you can either post your ldappl file for review with additional information on what you would like to see or open a case with support and they can help review this process with you.
I think I have found the problem (but not the solution)
I don't know why but Internet Explorer custom data is now working but for my other custom registry key (in HKCU), when I launch inventory with /f switch, data is insered. (data are also presents in log)
When automatic inventory is launched, data is deleted.
Is there a way to add /f in client ?
Keep in mind that scanning any HKCU value will potentially have unpredictable results in inventory. the issue being that the inventory scanner may execute when a user is or is not logged on to the system. In the event that the latter scenario occurs HKCU will be unavailable at a time when a user is not logged on, and will not return the data to inventory. This might cause the data to drop out of inventory on a device. Also, if the inventory scanner is running in system context HKCU doesn't reflect the actual logged on user's user hive, but rather reflects the system's user hive, which might not even contain the data or may have different data. I would potentially suspect the former not the latter in your scenario.
a suggested solution for unpredictable problems with an HKCU value.. If you can do this, devise a way that when a user logs on, a script executes (maybe GPO or logon script), and very quickly copies this HKCU value to an HKLM location. (Make up some special key for your custom registry collection) Then design the custom data entry around that location instead. This way your inventory scan will always succeed in getting this data.