There is a hardcoded limit of 4000 poles, which generates the intersection message you are seeing. The number of intersections is proportional to the number of poles squared (n*(n-1)/2), so 4000 poles generates 8 million intersections. As Dips is a 32-bit program, memory usage is limited, so we had to put a limit on the number of intersections that are calculated.
For now, the only way around this is to reduce or filter your data below 4000 poles in order to compute intersections.
Note: The Dips Query option is very powerful, and you should be able to create sub-set files using the Dips Query (Analysis > Query Data) or you can use Excel and then Copy/Paste.
There is another option in the Preferences dialog (File > Preferences) which allows you to control the number of intersections which are displayed. The default is 30,000. This is to prevent the entire stereonet from getting obscured by the intersection points, which tends to happen with large files. However, this option is independent of the 4000 pole limit, which cannot be user defined.