VPS conflict with actual MT4 program

Ok so I have the Gallantfx vps and it comes with a free MT4 web-based platform. What im concerned about is if my VPS is running on the webbased MT4 and I log off to let it run on the system, can I still open up my normal MT4 program and log into my real account and make changes? So far I’ve noticed the changes I make on my MT4 webbased platform are not showing up when I log into my real account on the nor MT4 program. Any ideas?