Pico,
Glad everythings working now. You were looking for some out of the ordinary stuff, which is why it took so long to come up with a solution.

Thought I would post the finalized code, just in case anyone else has to deal with something similiar.

[vba]
Dim wb As Workbook, ws1 As Worksheet, ws2 As Worksheet
Dim pb As Workbook, ps1 As Worksheet, ps2 As Worksheet
Dim StartLine As Long
Dim HowManyLines As Long
Dim response As String
Dim s As OLEObject

'Set references to the Master workbook
Set wb = ActiveWorkbook
Set ws1 = wb.Sheets("JOB_SPEC_FORM")
Set ws2 = wb.Sheets("PARTS1")
'Add new workbook
Set pb = Workbooks.Add
Application.ScreenUpdating = False
'Unhide job_spec_form
Sheet1.Visible = xlSheetVisible
'Copy data from first sheet, set reference to it and hide original workbook again.
ws1.Copy pb.Sheets(1)
Set ps1 = ActiveSheet
Sheet1.Visible = xlSheetHidden
'cycle through shapes and remove link
For Each s In ps1.OLEObjects
If Left(s.Name, 6) = "CheckB" Then
s.LinkedCell = ""
End If
Next s
'Copy data from second sheet, set references to it and copy and paste values
ws2.Visible = xlSheetVisible
ws2.Copy , pb.Sheets(1)
Set ps2 = ActiveSheet
ws2.Cells.Copy
ps2.Range("A1").PasteSpecial (xlPasteValues)
ws2.Visible = xlSheetVeryHidden
ActiveWindow.DisplayGridlines = False
Application.ScreenUpdating = True
'response = "False"
' Do Until response <> "False"
' response = Application.Dialogs(xlDialogSaveAs).Show
' Loop
Application.Dialogs(xlDialogSaveAs).Show
pb.Close False
[/vba]