97Civic123,
Nope, that sounds like something else to me. The clutch MC won't care what gear you're going into. I know I have to nurse my wife's Civic into reverse, I'm assuming the linkage is a little screwey.
But consider this, you have to "inputs" into your tranny...the clutch and the gearshift. All that the clutch pedal does is to enable you to change gears. If you have no problem changing into other gears, I'd lean towards poking around with the linkage for first.
Bogatyr