I have had this with a pair of used boots before.
Also, following on from what Gunwharfman said above, it could be that you are micro-tearing and/or inflaming a muscle. This could be that your arch over time has sunk i.e. you have become more flat footed, and so your inner part of the leg is now rubbing on side of boot....just a guess.
An easy/cheap way to see if this is the issue is to buy some new insoles with a decent sized arch support; you can buy these from most sports shops and sometimes even Aldi/Lidl. Cost about £10 a pair but got to be cheaper than a new pair of boots, and is it doesn't work you can always use them in a new pair of boots or shoes.
Be interested to know if it works.