This isn't a bug. This is the default behaviour for jetpacks in IndustrialCraft. Unless you wear advanced, or not so advanced, armo(u)r, you take fall damage, even if you fly up only a few blocks.
Best thing to do is make some rubber boots. Look it up in the IC2 wiki or on NEI if you want to know the recipe.
Other option, if you're at the end game level, is to make the Quantum boots. Again, look it up on the wiki or NEI if you want to know the recipe.