Never copy and paste graphics into Pagemaker (PM), it leads to all sorts of problems. Save your excel files as pdf files and place them into PM. Make sure you save the pdfs files as Acrobat 4 pdf files, PM cannot handle any of the newer versions of pdf files. I would give the same advice for your equations, it's best not to copy paste, but to save the files as .eps files and place into PM.
That's a lot of equations and tables for a program that doesn't handle them well, I would suggest looking into software that can handle it, like Framemaker or Indesign with an equation plugin. Ther are much more deficient workflows for that type of publication.
I am actually not copy pasting it. Copy -> edit -> paste special. I am doing it for the last 8 years and never faced this problem. Thousands of tables are created in this way in pagemaker. But recently i observed this problem that no right border and bottom border for a table. Is there any fix?
Windows 7, PM 6.5, Excel 2003
Same difference on the copy paste vs paste special. This involves Microsoft OLE linking, which is famous for working for a while and then suddenly not working right or not working at all. Add to that Windows 7 which is not supported by PM and you have a recipe for disaster.
If you want to continue on this workflow, I can only suggest a workaround, create a thick border in excel and crop in PM.
As said above, forget Paste Special. It was only ever part of PM to gain Windows compliance.
See Section 4 of the PM FAQs "Tables" - www.bigjohnd.org.uk/PM_FAQs/PM_FAQs.zip
However the long term solution is move to InDesign.