This isn't a problem per-se. A change to the load order methods is probably a good thing, as Bethesda's system is quite out-dated now. However, it does mean that any mod managers using the old method of ordering mods are not going to work without changes once the changes from patch 1.4.26 are committed in earnest.
With this in mind, WrinklyNinja of BOSS fame has written a comprehensive thread both here and on the official forums that helps to explain what load ordering is, what's changing and what this means for all of us.
Perhaps most pertinent is the following information:
The solution agreed on by Lojack (Wrye Bash), Kaburke (Nexus Mod Manager), WrinklyNinja (BOSS) and Dark0ne (owner of the Nexus sites) was that total load order would be stored in a "loadorder.txt" file, itself stored in the same location as "plugins.txt". "plugins.txt" would be kept in synchronisation with "loadorder.txt" so that the order of plugins that the game loaded was the same for both files, but the latter would allow the load ordering of inactive plugins.
Modding utilities would then perform their changes on "loadorder.txt", updating "plugins.txt" to reflect any changes to active plugin load order as required. This provides a common store for the total load order in lieu of the plugin timestamps used by the other games.
The bad news: Any utilities that you use to manage load order may stop having any effect. This is because nothing currently released knows about the change in load order system. In time, utilities may be updated to handle the new system as their programmers become aware of it. Until then, Skyrim's launcher is the only way to change load order.
One very important thing is that if you have a utility that can handle the new system, do not use Skyrim's launcher to set load order. This is because it doesn't know about the total load order, so if you change the load order through it, only the active load order changes and synchronisation between the two is lost. The only way for a utility to re-sync the two load orders is to undo the changes you made in the launcher.
With many thanks to WrinklyNinja for all the hard (and extremely fast) work coding the new load order system, the plan is for NMM and Wrye Bash to use the BOSS API to handle load ordering. This will naturally mean that NMM will have the added bonus of having some of BOSS's great functionality and best known load orders implemented straight in to the program as well.
We do not know when the beta patch from Bethesda will go live (one assumes it will be this week at some point), but I highly recommend you go and read WrinklyNinja's thread for the full scoop. Similarly, you will want to keep an eye out for Nexus Mod Manager updates and download them as and when they become available, because once the new beta update goes live the current versions of NMM will not be able to manage load orders at all. Which is bad.
Many thanks for WrinklyNinja for not only his hard work coding the BOSS API, but also his hard work documenting it all as well. Be sure to thank him yourself as well. Probably best to do it in the comments rather than PMing him; I don't want to be responsible for filling his PM box!
Pass the word on folks, because I'm sure we'll be getting many reports of NMM being "broken" because of this change until everyone is updated to the latest version.