There are a couple of graphical differences between jDOSBox and DOSBox:
Number 1:
For whatever reason, in our version of jDOSBox the window of jDOSBox does not look the same. It seems to be enlarged instead of being the correct size like the normal DOSBox.
See here (The correct size is to the left whereas our version is to the right):

I don't know where or why this was changed, but if you download the latest release (jDOSBox version 0.74.28) of SourceForge, the window is the correct size.
This wasn't caused by us. Some commit after release 0.74.28 (I don't even know where that release is at in the commit history) must've caused it.
Number 2 Solved:
Operating systems in general are different
A: Because of the weird window enlargement, it causes the graphics to look less quality.
B: In Windows 95 general glitches appear for example weird yellow lines appear on the screen and the dos prompt is messed up and shows almost nothing (just the cursor blinks and it doesn't show in the picture because I couldn't time it right)
Also, this issue is not DOSBox parity because I just tried Windows 95 in DOSBox, and let's just say it's not optimal (the black box is the mouse)
DOSBox:

jDOSBox (at least it's not as bad as DOSBox):

Number 3:
This one is the newest problem. When I try to go from 480x600 or whatever the default setting is in video to 1200x1600 I think it is. It says it was unable to take affect. Not sure how this could be fixed, but it works in DOSBox
There are a couple of graphical differences between jDOSBox and DOSBox:
Number 1:

For whatever reason, in our version of jDOSBox the window of jDOSBox does not look the same. It seems to be enlarged instead of being the correct size like the normal DOSBox.
See here (The correct size is to the left whereas our version is to the right):
I don't know where or why this was changed, but if you download the latest release (jDOSBox version 0.74.28) of SourceForge, the window is the correct size.
This wasn't caused by us. Some commit after release 0.74.28 (I don't even know where that release is at in the commit history) must've caused it.
Number 2Solved:Number 3:
This one is the newest problem. When I try to go from 480x600 or whatever the default setting is in video to 1200x1600 I think it is. It says it was unable to take affect. Not sure how this could be fixed, but it works in DOSBox