The upload speed depends on factors like how are you connected to Azure (Public IP or VPN or Express Route), how is the traffic flowing (hops to reach the VM) and also depends on issue with ISP (incase if it is happening occasionally).
As this needs deeper investigation, I would recommend to open a support case for this issue. A dedicated support engineer can look into the issue with analysis of packet capture.
If you don't have the ability to open a technical support ticket, you can email me with Subject as "ATTN: Vikas" at "AzCommunity@microsoft.com" and provide me with your SubscriptionID and link to this thread. I can then enable your subscription for one time free support.
Also, once you get the issue fixed, request you to reply back here on the thread with the resolution steps for the benefit of the community.