Box.com automation and file storage

We are uploading a ton of files daily. We got box so it would auto upload them there as mass downloads in Quickbase are not a thing (which sucks)

We have a folder for each client. Then when we add a new car (we are an auto shop) it has an RO# associated with it. Box makes a new folder in the clients folder using that RO# ever time we add a new car to Quickbase (its a table)

That in pipeline works perfect. Instant folder that is named after the RO# for that car. Awesome. 

But when I put in the pipeline to then upload the new documents that the user uploaded to that new folder... it fails. 
If we wait like a day or so, then upload they seems to work then. it's like pipeline and box talking to each other has an issue with files instantly created. If I tell pipeline just upload it to the client's folder it works. But then we have 100s of files not in their correct RO# folder. We have to manually move them and its sucking up a ton of time. 

we also cant wait a day, this needs to be almost Realtime.

Any thoughts on why it fails with newly created files?

Thanks!