If I understand you correctly -

The size of the window has to be greater than a critical defect size, otherwise the bone will regrow.  So perhaps a larger window.  See this article regarding sizes in different animal models:

http://www.sciencedirect.com/science/article/pii/S2214031X15000388

Also, have you tried Loctite glue?

It sounds like what you are experiencing is dura re-growth. Its my understanding that, the more bleeding/trauma that occurs during surgery, the more dura re-growth that will occur. This has something to do with immune response bringing bone cells to the area - similar to what happens if you fracture a bone and the fracture site eventually develops a larger bone mass in that area than was there originally. I would work on reducing bleeding and trauma during surgery. You also want to make sure that your artificial dura is covering sufficient area, or else dura re-growth will creep into the window site. 

Thank you for your responses. The following picture shows the tissue regrowth right after the window has fallen off: http://imgur.com/a/j1cEd (notice the whitish tissue on the right side). We will look into using a larger window size. We have not tried Loctite glue although the window has stopped coming off when using Metabond (the tissue regrowth remains). We notice that this happens even in mice with very minimal amounts of bleeding but we will try to reduce bleeding as much as possible.

If you have not yet found a sufficient answer to this question, you can try the following:

During surgery:

- Assure proper aseptic technique of the whole surgical area (including scrub down of the area and all applicable surfaces with appropriate cleaner).

- Heat sterilize all of your surgical tools, plus use an added step of sterilization with 90% ethanol.

- When the skull is exposed, and area properly anesthetized with topical anesthetic (e.g. bupivacaine), use an alcohol scrub of the skull and surrounding cut scalp tissue, followed by scrub with an iodine based solution (e.g. Betadine), followed by an additional scrub with ethanol.

- Prior to drilling the window itself, lightly remove a surface layer of skull off of the entire skull surface. After completing this, "golf ball" the entire surface of the skull. Cool the drill often while making these divots on the skull. This process allows the glue to adhere better to the skull surface. Scrub the skull surface once again after the golf ball procedure.

- Prior to commencement of surgery, use dexamethasone to reduce brain swelling and post-surgical complications.

Steven Hou , please, could you share how you solved the re-growth of bone in your windows? I am experiencing the same problem...