It's probably just the overlapping edge itself causing the thump. My main commuter bike has a slight ding in the rear wheel that gives the same effect - and it's just about noticable if one spins the wheel and watches carefully.
Incidentally, what prompted you to try the tyre liners? I commute about 18 miles each way and save for the fact that my rear tyre is getting a bit worn (could have been a contributing factor in last night's flat) I have minimal problems Tyres are 700x23 Conti sport 1000.
Ed
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Get a bicycle. You will certainly not regret it, if you live.