Since I've been waiting for a stable version of 1.6.1 from Bukkit there has been a quite a few bug reports that are being resolved by Mojang. It may cause issues with getting a stable version of 1.6.1
Here's the bug list for just the vanilla game (which makes modded games even harder to fix >_< )
[MC-149] ? Powered pistons drop as items in creative
[MC-1545] ? Player's and Horses head while riding having strange behaviour when looking at the skin in the inventory
[MC-2025] ? Animals going out of fenced areas/suffocate in blocks when loading chunks
[MC-2840] ? Chat concurrency issues
[MC-2841] ? Packet flood degrades server peformance
[MC-5770] ? When putting a sign in front of water it keeps running
[MC-7486] ? Trapped Chest looks like Regular Chest in inventory / item frame
[MC-12962] ? Attacking wild Wolves with any kind of projectiles (Arrows, Snowballs, Potions) will cause any nearby tamed Wolves to attack their owner
[MC-13167] ? Reloading a world while player is in moving Minecart or riding a horse is glitchy in F5 mode
[MC-13632] ? Horses can be pushed into blocks and then take suffocation damage
[MC-13695] ? Ctrl+Click = Right Click on Mac not working
[MC-13949] ? Leads attached to mobs drop as items when right clicked in creative
[MC-14157] ? Numlock Enter not recognized as Return
[MC-14359] ? Direct Connect does not remember port
[MC-14415] ? rope part of the leash turns invisible in some angles
[MC-15024] ? Hay blocks can not be crafted back into wheat
[MC-15161] ? Gliding crosshair when on a saddled horse
[MC-15547] ? "Nether-Fortress-Only" Mobs no longer spawning in previously generated Fortresses
[MC-16170] ? Unarmored horses appear as wearing diamong armor
[MC-16222] ? Baby Zombies are far too fast
[MC-16267] ? Cannot change Horse Armor like Player Armor by clicking with another armor piece on slot
[MC-16761] ? Sprint does not happen straight away
[MC-17673] ? Distorted fonts when using a converted texturepack on startup
[MC-18365] ? Breaking sound and particles appear when placing water/lava into another source block
[MC-18627] ? The "clear" command is causing a player in creative mode to be unable to move items in their inventory.
[MC-18828] ? /clear command causes problems with animations of held items
[MC-18976] ? Health boost resets additional health every 30 seconds
[MC-19082] ? Signs placed on Fences don't have Text
[MC-19585] ? Trying to jump on an unsaddled Horse, then equipping it with a saddle makes the Horse jump automatically
[MC-19592] ? 1.5.2 clients show server 1.6.1 as 1.3 in Multiplayer screen
[MC-19599] ? Item Dupe
[MC-19605] ? the /playsound command does not work with @a when >1 player passes the query
[MC-20050] ? Minecraft 1.6.1 demo has crashed
[MC-21145] ? Demo crashes when unable to find 'name' of a bound mousebutton
[MC-21172] ? resourcepack crashes
[MC-21436] ? nested colors in json chat don't work
[MC-22315] ? Item Duplication by Mules/Donkeys
[MC-22401] ? Cannot pick block lead in creative.
Source