This is a known issue. Smart Groups are working exactly as designed but they were not really designed to be created from Online/Remote Searches. There is just too much variety in field names and mapping for this to result in anything other than the types of issues you are seeing. It was a design oversight that the “Smart Groups” option is even available in this context. We are working on changing this for the upcoming X2.01 patch.
In EndNote X2, “Smart Groups” are supposed to be created against a local library/search - not against Online Searches. To create a “Smart Group”, choose Groups > Create Smart Group. This opens the “Create Smart Group” dialog. Here you can enter search criteria that can be saved. Once created/saved a Smart Group will be active for your library. Every time something changes in your library that meets the criteria of your Smart Group, it will be updated automatically.
For a very simple example, if I create a Smart Group for Author name “Rollins”, every time I add a new record that contains this author name to my library, it will also automatically get added to this Smart Group.
So, anything added in a web search to the main library will not be automatically added to the smart folder? Technically, web queries are automatically added to the main library, so I am unsure of why this is a problem for the smart folder.
Any new records added to your library - from an import, online search, etc will be included in a Smart Group presuming the group criteria is met. The issue related to Online Searches discussed earlier is slightly different.
You actually have two options for creating Smart Groups - one is to create from the Groups menu. The second option is to perform a search - online or local and then choose “Convert to Smart Group” - meaning “convert this search strategy to a Smart Group in my library”. This was not designed to be used when doing an Online Search. There is a bug in EndNote X2 that allows this when this option should not be active. This bug is relatively harmless but can result in odd results particularly when converting a search against PubMed to a Smart Group because of the way fields are named and mapped.
In the upcoming X2.01 patch, we are disabling the option to “Convert to Smart Group” from Online Searches as we had originally intended to.