Sounds like the tool codes either aren't in the file or arent loading properly. It is working for me fine over here so I would suggest a few things...
1) Try running the Excellon.cam file in the install rather than a custom file. Also try this on one of the examples in the build (I used the TI Launchpad just to ensure it was something more interesting than say, the Hexapod). See the settings in that CAM job file:

2) Failing that, please open the generated Excellon file...the top of the file should look like you see below:
%
M48
M72
T01C0.01200
T02C0.03600
T03C0.04000
T04C0.11000
%
T01
X53629Y32100
X67129Y41600
X63129Y46600
X59129Y59200
X69129Y60100
X60329Y69600
X59929Y80200
...if it doesnt include the much-needed toolcode data (the lines beginning T0<n>C<m.n> are your tool codes and have the diameters of the tools needed by viewmate) then viewmate may still have the drill hit info seen later in the file and marked by X<m>Y<n> but not be able to assign specific tool codes to the hits. This could result in your "?"'s which are essentially undefined tool codes in Viewmate.
2) If the file looks ok, then please load the file in Viewmate and then go to Setup -> Toolcode... If the first few "T" numbers are empty, then the tool info is not being imported. Please send over the detail on what version of Viewmate you're using. I'm using whatever the latest is on their website (updated just to be safe).
3) Also feel free to send over the excellon file. You can post here or just email me directly at matt.berggren@autodesk.com and I'll have a crack at loading it on my machine. I may need the PCB if the file looks screwy but I'll let you know. If you feel comfortable emailing it preemptively, then shoot it thru. Just send to me directly.
Best regards,
Matt - Autodesk
Director of Fusion Electronics
Autodesk EAGLE