I can only come up with one more suggestion, but it'll take more work ... if it works. But I suspect it will ...
Rather than create a single PDF from the combined book, create PDFs from the individual INDD files, then stitch them together in Adobe Acrobat.
Since you've identified Chapter 3 as an offending party, we can experiment by stitching the first four chapters together and seeing if it'll work:
- Create PDFs of the first 4 chapters from the INDD files.
- Open Chapter 1.pdf in Adobe Acrobat.
- Navigate to the last page in Chapter 1.pdf (optional, but faster to confirm this is working). Then select the Organize Pages tools, then the Insert>From File... ccommand in that section.
- Select the Chapter 2.pdf file. When the follow-on Insert Pages dialog box appears, select After in the Location: edit box and the Page radio button under the Page section, then click the OK button.
- This should place the first page of Chapter 2.pdf after the last page of Chapter 1. Navigate to the new last page, then lather-rinse-repeat with Chapters 3 and 4. This should get you the results you're looking for — no ifs, ands or buts.
- Save the PDF as Chapters 1-4.pdf and admire your handiwork.
Now before you go further, there may be an easier option. Close the Chapters 1-4.pdf file, and select the Combine Files option to create a combined PDF. Since this is quick, you can do them all and see if you get lucky. Navigate your way to the folder containing your 25 separate PDFs, then use your Shift and/or Command/Ctrl keys (depending on whether you're on a Mac or Windows system, respectively) and select the PDF files in numerical sequence. Just using the shift key to select them all can introduce some rude pagination surprises.
If you're lucky, the second workflow will get you what you're looking for in the resulting Binder 1 file which you can save and name anything you want. But if you're not, the first process I outlined should work every time.
Good luck,
Randy