The next version of the BatchPreprocessing script will have the automatic probing feature disabled by default, so this problem will be fixed (Rationale: In a batch image preprocessing task all frames should be registered in a single attempt. The automatic probing feature of StarAlignment has been designed to help register images in very difficult cases, mainly in cases where there is very little overlap between images, or strong scale differences. These cases should never occur in a batch preprocessing task).
For now, a workaround is patching the script. This is actually very easy, but requires you to edit one of the script's source files:
1. Locate the folder where the script is installed. On Windows, this should be:
C:\Program Files\PixInsight\src\scripts\BatchPreprocessing
On OS X, the folder is within the PixInsight64.app application bundle. Right-click PixInsight64.app and select "Show Package Contents", then navigate to the src/scripts folder inside the package.
2. Copy the BatchPreprocessing folder to a location where you have write permission. For example, a good place is your Documents folder under your home folder.
3. Open the Script Editor window in PixInsight.
4. Select File > Open (from the Script Editor menu, *not* from PI's main menu).
5. Locate the folder where you have copied the BatchPreprocessing folder in step 2.
6. Open the 'BatchPreprocessing-engine.js' file
7. Press Ctrl+F (Cmd+F on OS X) and search for "new StarAlignment" (without the quotes). It should be around line 940 of the script (sorry, I don't have the same version that you have right now, so I don't know the exact line number).
8. After "new StarAlignment", add the following line:
SA.maxStars = 2000;
Take a look at the attached screenshot, where you can see an example.
9. Save the script by pressing Ctrl+S (Cmd+S)
10. Now you can run the modified script by selecting Script > Execute Script File from the main menu, and selecting the 'BatchPreprocessing.js' file from the folder where you copied the script in step 2. Note that the modified script is no longer available from the Script > Batch Processing menu, since it is not featured.
Hope this helps.