I'm not sure if I've totally understood your issue, but I'l give you my take.
In all honesty, speed-testing your connection will only ever give a meaningful result if you don't have anything else using that connection. You have a finite amount of bandwidth, both up and down. If you have any software running that uses some of that bandwidth then you're more than likely going to see your results drop.
To give you an example, for the last 4 years I have suffered under the yoke of an old copper-wire ADSL connection. It started out at about 12Mb/s and has "improved" recently to around 17 or 18. If I have torrents downloading then I can forget using the internet for ANYTHING else. Netflix? Nope. YouTube? Nope. Checking emails? Nope. If I want to stream a film or anything then I have to pause or exit my client until I'm finished. Same thing if I even just want to check the forums or refresh a page.
As for why you're seeing different up/down speeds in your client, I'm not sure. I use BiglyBT, and it seems as though the speed counters are displaying an average speed over the last 30 seconds to a minute rather that the actual speed at that precise moment in time. To get a better idea of where my bandwidth is being used I tend to open Resource Monitor and look at my connections in there, as I can sort them all by current speed.
On the plus side, after fighting to get fibre here for years, they're coming first thing in the morning to connect me. I'll be interested to see what I actually get on my new 500Mb/s line.