The problem, in case you're technically curious, is that the server filters the damage values on block items which are believed not to have durability or subtypes. This includes monster spawners, even though it would be very useful to store the creature type in the item damage value – as Not Enough Items does (and I imagine Too Many Items too). Bukkit used to allow this but the change was reverted in 1.0.1. Here's the bug: https://bukkit.atlassian.net/browse/BUKKIT-329
Fortunately it was fixed in 1.2.4, so future major versions of Tekkit are likely to not have this problem.
Until then, it is possible to workaround this problem in several different ways. You can use my Bukkit plugin, SilkSpawners. Unfortunately it isn't as convenient as using NEI/TMI, but you can acquire spawners using the /ss command (i.e., /ss skeleton), change their type, etc. I originally wrote this plugin to let you pickup mob spawners using Silk Touch tools, but it turns out to be very useful to manipulate spawners in general. It will even work with custom mobs added by other mods.