BG's are a resource in, resource out bank.
It doesn't matter how you play them. Kill efficiently and it will just take more BG's to fully load them and the number of BG's between payouts will increase. Kill them inefficienctly and the gap between payouts will decrease. But they still track resource in and resource out (apart from the top level caveat noted below).
So, if the game is functioning properly, its not possible for a player to consistently get back only 70% of what they put in, over a long period of time.
If you track your loading and payouts (as the resource of the troops, which includes food) you'll get the 3/4% losses/tax that people talk about. FYI I have done that over thousands and thousands of BG's.
You'll have to do it over many many many cycles (loading then clearing via a full payout), as the type of troops loaded can affect each individual cycle, you can get partial/half payouts and other vaguaries. But any under/over on each cycle just stays in the bank and affects future cycles, so it all washes out eventually. You just need to take a big enough sample.
Note that all the above goes for playing the BG's "normally". If you haven't reached the max level yet then each time you kill a top level BG a different mechanic applies and you will see different results from your resource tracking.
If you truely are getting only 70% back then you are experiencing some king of bug. I recommend you track your resources for an extended period of time.
More than likely you will prove the above to yourself (3/4% tax). But if you don't you will have the evidence to start a support ticket and hopefully get it investigated.
It's possible that the gear issue (I have heard others say that gear stops coming but never done that many on a single account in a day to see it myself), doesn't just affect the gear but also stops the bank tracking resources.
The max lvl of BG's used to be 60 but I think it's now 100. That matches up to your experience of the gear stopping at 100 BGs. But this being the bug ridden game it is it's possible to get yourself in a position where you have more BG's than the max theoritically allows. Maybe this could this could cause a bug?