I think I read about this in one of the Tech Corners at Planet Half-Life.
The problem is when the level load it puts you into the floor instead of on the floor thats why you take damage and die.
I think the solution was to repeatedly press the jump button while the level is loading in hopes that it puts you above the floor...either that or use "god mode" and no clip your way out of the floor.
EDIT:
Here is the Tech Mailbag concerning the issue
__________________
| CPU: Intel Core2Quad Q6600 (G0) @ 3GHz | GPU: MSI 8800GT 512MB | Memory: 4GB (2x 2GB) G-Skill DDR2 @ 1000MHz Dual Channel | Monitor: Viewsonic Q20WB 20" LCD @ 1680x1050 | Operating System: Windows Vista Home Premium x64 |