I had the same thing happen to me when I curiously poked the slave cylinder's piston back in further than it normally goes. The pedal just dropped to the floor but it worked as soon as I pulled it back up.
Here's what I think happened: by pulling the tranny back, that pushed the slave cylinder's piston back in more than it would normally go. Upon getting everything back together the slave cylinder's piston probably wasn't touching the clutch release fork. When you pushed the clutch pedal down the first time, the piston moved out as much as it would on a regular stroke but because it was retracted a bit, it just started touching the release fork at the end of the stroke. The pedal stayed on the floor because the release fork couldn't physically push it back. By pulling the pedal up, hydraulic fluid gets sucked back into the system which allows the slave cylinder's piston to push out even further on the second stroke. At this point you can start properly "building pressure".
I hope this makes sense...
TL;DR: I think your clutch's hydraulic system is just fine.