Unfortunatly yes this is an issue, here are some potential workarounds:

One workaround would be to, of course, make the tool visible as specified in a custom layout. However, if the user starts up with a layout that does not include the tool, then FbxRetrieve will not be called unless the tool is made visible and the file is reopened.

Anothr one is to use a class derived from FBUserObject in conjuction with your tool. See the ortoolpersistent sample. By placing an FBUserObject, which has its own FbxStore and FbxRetrieve, in the scene, you can place the data you need in some intermediate place, i.e. the user object, such that when the tool is made visible, it can retrieve the data from the user object. Without the user object, there’s no way to obtain the data from the FBX file until you make your tool visible and you reopen the file (which forces FbxRetreive of your tool to be called).

~Kristine