Question Need help with a serverside backend app

Ok so i have a project where 90% of the functionality is handled on a website and database.. but i need to have a webgl player display a single scene. I've worked out that i need to have an app that runs on the server side of things, automatically, and "prerenders" the scene, saves applicable information to the database, and then the webgl player will reconnect, get the applicable data from that file, and render the scene to users from that data set.
Where i am running into issues is the "prerender" app. If im in the editor and run it as if it were the full webgl app it works fine. It does what its supposed to do with the database. With in seconds all the data on the db changes properly. But when i compile it as a server app so that it can run headless/nographics, it takes 2-3 minutes for changes to be made to the database. I tried stripping out all the visuals and super simplifying the code to no avail, to the point where i broke it entirely and now instead of it taking minutes, it just do anything... (thankfully i made a backup)
This obviously in the proof of concept phase, and ultimately would like to build one app that just runs continously on the server instead of opening and closing, but i cant move on to that until i figure out why it might be taking so long to post results vs the in editor app.
It also seems to make a TON of connections to the db compared to the in editor visual version. Like 100s compared to 4-8. Any idea why would that be happening?