I get that "jumping back" too, with Microsoft Excel, but not with SH3
Here's my d3d9.ini file. I've been using InfiniteScreen for so long that I can't remember anymore what was the situation with this file back then.
[GLOBAL]
DebugLog=false
[ENGINE]
DisplayWidth=1366
DisplayHeight=768
Refreshrate=false
[LOADSCREENS]
tx=0.01635
ty=0.0
sx=0.0
sy=0.00
maxscale=true
[EFFECTS]
Ocean=false
Are your DisplayWidth and DisplayHeight set to the size you want to use?