There are a lot of responses here which I don't have time to read them so if what I say is a repeat from someone else, sorry! LOL!!
I suggest you NOT upgrade the bike, keep it as it is because the quality of the bike is a basic beginner bike and you'll waist money trying to make it something it's not. While yes spending another $200 or so more than your bike cost you new, to get another bike won't buy you much more than what you have now, so instead of upgrading, save up more money till you have around $1,500 but you may not have to spend that much depending on what you want. The Masi Vincere Disc comes with Tiagra which is really darn close to what 105 is now so it will be a quality groupset, and the bike is only $1,100. Another perhaps even better deal is the Diamondback Century 3, this one comes with the 105 shifting system and it retails for about $1,100. Also the Specialized Allez Elite is another 105 bike for a bit more than the above two at $1,200. Giant Contend SL might be the lightest option with 105 components, but it will the most expensive at $1,450. And the last option is the Trek Emonda ALR4 with comes with Tiagra for $1,150. Of the ones I mentioned the Diamondback has a bit more relaxed riding style than the others so it would be the most comfortable of the group for riding long miles riding comfort; and personally I like the looks the best too because it has a more graceful flowing look, and it does not have just boring black or some boring shade of gray paint on it that's on 90 percent of all bikes made.
It might be the cranks - it might be the spindle, but it's all torqued to spec and i even replaced the no-name BB with a shimano unit to see if that was the issue, but the problem only occurs once you go 600W+ so it must be down to flex somewhere! Never had this issue with the 5800 crankset + BB on the same bike.
