Well, I'm assuming you have some sort of script going off whenever you're numbering. Like maybe you co-opted the "AutoIncrement" script example?
Well, I did that too. It totally craps out after you get about 1000 points- because it has to scan your entire dataset's values in order to determine which number is the maximum so it can autoincrement by one.
What you need to do is limit the number of points you send out to like 5-10 or so.
SO: When you check out of ArcGIS, make sure you only select those features which are vital to your workflow- those that might overlap with areas you're currently working in, and ALWAYS the last feature in your dataset, so that your autoincrement number properly increments.
Am I getting warm?