Purchased Syndicate recently and while it works fine, playing the game is a little annoying (not totally bad though) due to it being a little choppy and slow in the gameplay.
I tinkered in the settings gog provides; changing resolution etc but it only effects the menus not the actualy game. When starting a mission it always presents the same resoultion and aspect ratio even when the I un check the setting to keep the ogirinal aspect ration and when I change the resolution, scaling engine option or render option (Open GL etc.)

Additionally I heard that it was down to cycles that may be why the games is a little choppy. I alterd it in the dosboxSyndicate.conf file to 10000 and even tried to use to key combos in game (Ctrl+12/Ctrl+11) but there is not change.

Can anyone help me out here?

Are you referring to there being black bars on the top and bottom during missions, making it look like the game should be larger? That's actually how the game is during missions. The black bars are part of the picture. The developers didn't use all of the 640x480 screen, likely for performance/memory reasons, since that would've been awfully demanding of the computers at the time. You can see this if you press Alt+Enter to switch to windowed mode.

As for the cycles, I set them to "auto" in the .conf file and the game chooses "max." So, try "auto." If you want to use fixed numbers, though, I suggest starting at something higher, like 30000 and then changing the cycleup and cycledown values from 500 to 5000 or 10000, since the game has a huge range of 10000 to 100000 where it's still playable.

BTW, if you're willing to try, the open source FreeSynd project linked at the top of this forum will allow the game to play slightly larger in fullscreen and slightly more smoothly. I can't speak for how complete it is or if there are bugs. I've only loaded it up and played around with it for a few minutes.

Just change it to "cycles=auto". You could also do "cycles=max". DOSBox recognizes both words in addition to fixed numbers (ex. "cycles=30000").

Just figured out what to look for now. It doesn't help that the conf file is one massive wall of text, I though it said "autocycles". Was about to message when I pasted it into the gog message window and it paragraphed it auto matically.

Anyway, I'll mess around further and see the results.

The lines are run together and it's a wall of text because Notepad can't understand the formatting. Open the file in a different text editor (like WordPad or Notepad++) and the formatting should be correct. You might then copy all of the text to the clipboard, paste it into Notepad and save it so that it looks right in Notepad from now on, if you prefer using that.