What I have to do is keep the orignal title for both but at the end of the 
title put this in 

"Title 1x09 (1)"
"Title 1x09 (2)"

If you use media browser to play the show it will combine them and play it like 
it is just 1 file.

Yeah that's not really the problem. It's a single file containing two episodes.

I had to manually rename the file to get it to work.
Example Star Trek, Deep Space Nine - S01E01-E02 - Emissary
 The S01E01-E02 is the key. Once I did this MCM was able to fetch. So in you can you will need to manual add 1x11-12 to get the fetch info.  

That's not really the problem either. I had the file named 1x11-12 or whatever 
but when I pick auto rename it doesn't maintain that. So for example if I have 
a file called Show 1x01-02 it would rename it to Show 1x01-02 Episode Title 
1-Episode Title 2 or something along that line.

I think I understand. I have the ST Deep Space Nine. Season 1 the first two 
Episode's was actually a two hour premiere.

thetvdb.com shows it separate.

Star Trek, Deep Space Nine - S01E01 - Emissary (1)
Star Trek, Deep Space Nine - S01E02 - Emissary (2)

Since I had it in it's original two hour format I had to name it. 
Star Trek, Deep Space Nine - S01E01-E02 - Emissary

But when MCM fetch the info it renames it.   
Star Trek, Deep Space Nine - S01E01-E02 - Emissary (1)

Since it is combine you want it to look something like "(1,2)" or do you just 
want the "(1)" removed?

Ah I finally see what the problem is.

My original problem was my naming convention was as follows 1x01 for single 
episodes and 1x01-02 for double episodes. It seems that MCM doesn't like that 
as a double episode format. It wants 1x01-x02. When I do that it successfully 
sees it as a double episode. So I guess the original bug would be to not 
require the second x in that particular naming convention.

As for the point you just mentioned, yes I would like it denoted that the video 
file contains both parts of a double episode. Any of the solutions you 
mentioned would be fine. If the two episodes have unique titles then I guess 
amending both titles would be best.

It took me awhile to figure out the name convection too. Pete is a really good 
programmer but even he can't cover every possibility. :)  

I understand that, and I appreciate the work that Pete is doing too, I just 
thought it would match the regular expressions used in Sapphire and XBMC/Boxee.

[deleted comment]

http://forums.mediacentermaster.com/viewtopic.php?f=20&t=671

Fixed and waiting for next release.

Released in version 1.29.2711.620.