As MK says GTX liners can be fragile.
An other thing to try is SnoSeal, same sort of thing as Nikwax.
A tip I can give, what ever wax you use, try to put a bit of heat on to surface of boot, ( it MUST be complely dry). You could use a hairdrier on low setting, put on a window sill in sun, upside down on a raidaitor, not for too long, just enought to get a bit warm.
The leather will soak the wax deeper in if you can do so.