Using percentages to calculate how much capacity is left in the battery isn't an ideal choice. It's good for a very, very rough guide at the field but I wouldn't hang my hat on it.
How much are you putting back into the battery to recharge it? That's probably the biggest indicator. If you're flying for 2 1/2 minutes and chewing up 2000mah, you have a big problem. Have you put a wattmeter in line to see what kind of amperage you're pulling?
I will also say that lipo's inherently lose capacity as they age, so you'll notice you'll see your percentage at the end of the flight dwindle over time. I generally aim to have 25% left in the pack, and once it gets down to 20%, I pass them off to my RC buddies.
One final thing, there are a bunch of guys on RCGroups who have been testing battery packs of all brands and have tabulated the data, it's very informative. Thunderpower are some of the worst bang-for-buck batteries on the market.
Here's a link for the curious.
https://www.rcgroups.com/forums/showthread.php?1767093-Battery-Load-Test-ComparisonsThe whole thread is over 1000 pages long, so page one give you the cliff's notes.