PLT OF A CARGO C208B LEVELED OFF AT AN ODD IFR ALT INSTEAD OF AN APPROPRIATE VFR ALT TO WHICH HE WAS CLRED DURING DEP.

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I FILED AN IFR CLRNC FROM SMX TO ONT. I CLBED UP TO AND LEVELED OFF AT 11000 FT. I WAS TOLD A SHORT TIME LATER THAT I WAS GRANTED AN IFR CLRNC WITH A VFR ON TOP ALT. I WAS TOLD THE PROPER ALT WAS 9500 FT OR 11500 FT; A MISUNDERSTANDING. I'VE NEVER SEEN A CLRNC WHERE IF YOU CHOOSE TO GO IFR AND NO VFR IN THE WORDING YOU ARE GIVEN VFR ALTS. MY QUESTION IS WHAT IS THE DIFFERENCE BTWN SOMEBODY THAT IS VFR AND LEVEL 11500 FT; AND SOMEBODY THAT IS ON AN IFR CLRNC WITH VFR ON TOP AND LEVEL 11500 FT. I PLANNED TO ASK FOR HARD IFR ALTS IN THE FUTURE TO CUT DOWN ON ANY MISUNDERSTANDINGS. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: RPTR STATED THAT HE WAS A RELIEF PLT FOR THIS SCHEDULED CARGO FLT AND PICKED UP HIS ACTUAL IFR CLRNC IN THE AIR AFTER TKOF SINCE THE TWR WAS CLOSED AND ZLA HANDLED THE FLT PLAN WHICH WAS STORED WITH THEM. THE FIRST CTLR CLRED HIM AS FILED. HOWEVER; THE SECOND CTLR APPARENTLY DID NOT KNOW THAT HE WAS ON AN IFR FLT PLAN AND BELIEVED HIM TO BE VFR ON TOP. THEREFORE; THE MAIN PROB WAS WITH THE ZLA INTRAFAC COORD. THE MATTER WAS SUBSEQUENTLY HANDLED WITHOUT DELAY OR INCIDENT.