"Is this a problem of the same namespace?"
That may indeed be the correct term. This behaviour has been used to run multiple copies of the same top level VI at the same time. I have not done it personally but I believe the technique starts with an EXE created in LV and then copy it off as different names.
I understand that this is working against you!
"Is there any workaround?"
Try taking a look at this link (see below). In it I was supporting another engineer that was trying to interact will a VI from VB (using a VI in a dll). Jean-Pierre gave us some good feedback. The way I understood what was happening is this.
The VI's inside the dll (or an EXE) run in the memory space of the run-time engine. Some quick hacks I threw together indicated that I could n
ot see the VI's that where loaded in the development environment.
http://exchange.ni.com/servlet/ProcessRequest?RHIVEID=101&RPAGEID=135&HOID=5065000000080000002F920000&UCATEGORY_0=_49_%24_6_&UCATEGORY_S=0
If someone else wants to jump in here and offer a better answer,
PLEASE DO SO!
Offering what little I know,
Ben