Hi,
OK, I set my path to my mkmdl.parts.xml file (renamed due to using MDL Commander and Middleman).
Test 1: FSX Electra to FS9
I imported the FSX Electra with my reduced VC (that gave me a stable model before) and exported it to FS9. I loaded it directly from the opening screen. I got an immediate black screen with this error:
Problem signature:
Problem Event Name: APPCRASH
Application Name: fs9.exe
Application Version: 9.1.0.40901
Application Timestamp: 4135a208
Fault Module Name: ntdll.dll
Fault Module Version: 6.1.7601.24545
Fault Module Timestamp: 5e0eb751
Exception Code: c0000005
Exception Offset: 00034753
OS Version: 6.1.7601.2.1.0.768.3
Locale ID: 1033
I then loaded FS9 with a different aircraft first and switched to the Electra. This seems OK.
All of the mouse rectangles I can find (there aren't very many in this VC) appear except Feather Prop for engines 3 and 4 - engines 1 and 2 are OK.
All of the interior and exterior animations seem fine, including prop pitch. Happy days!
I then quit FSX and restarted, loading the Electra immediately. This worked OK. Perhaps a problem only the first aircraft load of the day?
Test 2: FSX DC-6B to FS9
I imported the FSX DC-6B (which had been converted by earlier versions of MCX from the original FS9 model) and then chose Export Object (FS2004 MDL). When I clicked OK I got an immediate error window stating that an Exception had occurred. I sent an error report to you, so you should have the info. It was Object reference not set to an instance of an object. No MDL file is created. When I tried it a third time the yellow While you are exporting... window remained on the screen forever, no matter what program I ran. I'm looking at it right now as I am typing this.

Quitting MCX removed it.
Test 3: FS9 DC-6B to FS9
This time I imported the FS9 DC-6B and re-exported it to FS9. All the mouse rectangles appear and work fine. However, my custom fuel levers and prop reverse bar do not have any tool tips, just the "hand" cursor. They operate OK, but with no tooltip to help you know what setting you are at. I did specify the path of my mkmdlparts.xml file which contains the info. The MCX modeldef file does not contain these entries.
Here is an example of the code:
XML:
<part>
<Name>lever_propliner_fuel1</Name>
<Animation>
<Parameter>
<Code> (L:TANK_SWITCH1, enum) 50 * </Code>
<Lag>100</Lag>
</Parameter>
</Animation>
<MouseRect>
<Cursor>Hand</Cursor>
<Tooltip_Text>Fuel 1: %((A:Fuel Tank Selector:1, enum))%{case}%{:0}OFF%{:1}ALL%{:2}Left%{:3}Right%{:4}Left AUX%{:5}Right AUX%{:9}Left MAIN%{:10}Right MAIN%{:13}X-Feed%{End}</Tooltip_Text>
<mouse_flags>LeftSingle+RightSingle</mouse_flags>
<Callback_Code>
(M:Event) 'LeftSingle' scmp 0 == (L:TANK_SWITCH1, enum) 2 < &&
if{ (L:TANK_SWITCH1, enum) 1 + (>L:TANK_SWITCH1, enum) }
(M:Event) 'RightSingle' scmp 0 == (L:TANK_SWITCH1, enum) 0 > &&
if{ (L:TANK_SWITCH1, enum) 1 - (>L:TANK_SWITCH1, enum) }
(L:TANK_SWITCH1, enum) 0 == (L:CROSS FEED1, enum) 0 == (L:CROSS FEED1 FAIL, bool) 1 == || && if{ 9 (>K:FUEL_SELECTOR_SET) }
(L:TANK_SWITCH1, enum) 1 == (L:CROSS FEED1, enum) 0 == (L:CROSS FEED1 FAIL, bool) 1 == || && if{ 4 (>K:FUEL_SELECTOR_SET) }
(L:TANK_SWITCH1, enum) 2 == (L:CROSS FEED1, enum) 0 == (L:CROSS FEED1 FAIL, bool) 1 == || && if{ 0 (>K:FUEL_SELECTOR_SET) }
</Callback_Code>
</MouseRect>
</part>
All interior and exterior animations are OK except for c_wheel (incorrect) and the water rudder (reversed). The prop pitch animations are correct. Adding lever_water_rudder to the animations INI file for animations to be reversed when going to/from FSX and FS9 does not change this reversal (which is logical since this is not an FS9 to FSX conversion).
Hope this helps,