You were only supposed to blow the bloody doors off! or words to that effect anyway!
Okay, so perhaps the gauge is faulty!
 Perhaps I should have first asked you how hard the tyres felt as there's a noticeable difference between 40 and 100psi. 
Have your tyres got presta valves? Those are the longer, skinny ones rather than the shorter, fat ones that mtbs (and cars) tend to have. Presta valves have a small nut on them that requires loosening first. Without doing that, you'll not get any air in the tyre.
The reason I said 'let some air out first' was that sometimes, even after loosening the nut on the presta valve, an air seal remains in the valve and prevents air getting into the tyre. The first couple of pumps normally break that seal... but not always. By letting some air out first, you ensure the seal (if there is one) is broken. I do it as a matter of course now. It's routine for me; unscrew the cap, stick it in my mouth, loosen the nut on the valve, tap the valve top to release some air, attach pump.
I have a Joe Blow pump too and it doesn't start requiring effort until around perhaps 90 or 100psi.
	
		
			
		
		
	
			
			Okay, so perhaps the gauge is faulty!
 Perhaps I should have first asked you how hard the tyres felt as there's a noticeable difference between 40 and 100psi. Have your tyres got presta valves? Those are the longer, skinny ones rather than the shorter, fat ones that mtbs (and cars) tend to have. Presta valves have a small nut on them that requires loosening first. Without doing that, you'll not get any air in the tyre.
The reason I said 'let some air out first' was that sometimes, even after loosening the nut on the presta valve, an air seal remains in the valve and prevents air getting into the tyre. The first couple of pumps normally break that seal... but not always. By letting some air out first, you ensure the seal (if there is one) is broken. I do it as a matter of course now. It's routine for me; unscrew the cap, stick it in my mouth, loosen the nut on the valve, tap the valve top to release some air, attach pump.
I have a Joe Blow pump too and it doesn't start requiring effort until around perhaps 90 or 100psi.
				
 Well I only put 95-100 PSI in my rear tyre and 85-90 PSI in the front (you need more in the back because more of your weight is on the back wheel). At just over half my weight, you really don't need to be going to that sort of pressure, especially for the crap road surfaces we have round here. Some of those aches and pains you're getting out on the road are probably caused by getting battered through rock hard tyres!