The missions you mentioned are working just fine in NewDark/FMSel. My guess is that your T2-installation is a mess. Did you use Darkloader? Then clean up the files first
http://www.ttlg.com/forums/showthread.php?t=48202
If this doesn't work, a clean installation with the latest Tafferpatcher is recommended. But never ever install Thief in a protected folder like C:\Programs(x86)
I'd also recommend to move the game out of the steam folder. Just copy+paste it wherever you want (but not in C:\Programs(x86) )
The pdf doesn't look pixelated on my rig. You can get the same informations about FMSel here
http://www.ttlg.com/forums/showthread.php?t=140093