Interesting stuff. A couple of immediate observations (which might be way off):
While the high OKW/Ostheer win rates (especially the OKW spike at the end) are notable, all of this data is from within one major patch (with a couple of small hotfixes). This means the big fluctuations in win rates are not neccessarily the result of balance changes. Perhaps significantly, each faction has at least one period of having the highest winrate (albeit a very small one for USF).
Ostheer winrate is generally pretty high, but they are the least played faction. Perhaps compared to other factions, Ostheer has a dedicated 'core' of players who know the faction very well?
Since OKW is far more played than Ostheer, the below-average winrates for Allies (especially USF) are mainly drawn from matches against OKW. This suggests that OKW is probably overpowered.
OKW win-rate improved in spite of the Kubel/munitions nerf. This suggests (at least to me, given my in-game experience) that tweaking the numbers on the Kubel isn't going to work - the unit needs to be reworked. The unit was originally felt to be under-performing and was buffed consistently to reflect this, but it seems that OKW players have realised how to use to Kubel to great effect, regardless of damage/suppression/RoF numbers.
EDIT: All this is looking at the 1v1 stats exclusively.
THe big day to day fluctuations in 1v1 are probably normal. players have their good days and bad days. However, the winrates of Axis in 3v3 and 4v4 are pretty consistent which probably means they are OP.
The creator of the program has posted data that covers a span of about 4 weeks (counting the days of his older posts). The past data are pretty similar to this currrent set, except OKW win rates have gone even higher, probably due to Kubel buff.