\includepdf[pages={34-40},nup=2x2,frame,landscape,scale=0.8,%
pagecommand=\chapter{fracture}\section{Theoretical}]{Dam-Nonlinear.pdf}
\clearpage
\includepdfmerge[nup=1x2,frame,landscape,scale=0.8,%
pagecommand={\section{blablah}}]{ASCE-Cyclic-Joint-Model.pdf,1,%
ASCE-Cyclic-Joint-Test.pdf,1}
\includepdf[scale=0.8,nup=2x2,pages={9-13},frame,landscape,%
pagecommand=\section{Experimental Work}]{Ageing-Shaking-Cracking.pdf}
\includepdfmerge[nup=1x2,frame,landscape,scale=0.8]{cement-concrete-slowik.pdf,1,%
Optical_Fiber-in-FPZ.pdf,1}
results in
- Correct header of chapter 1 (Fracture), and section 1.1 (Theoretical) and followed by the pdf file to be included (this takes two pages)
- First problem, on page 3, I get: Chapter 2 Fracture and 2.1 Theoretical again, followed by blank. Clearly wrong
- Then I correctly get section 2.2 blah blah followed by the pdf to be included (one page).
- I get correctly 2.4 Experimental work on the first of two pages, but again the same header of the second (of two) page.

pagecommand=instruction in curly braces? In the code you provide, you only appear to do so for the first\includepdfmergemacro, but not for the two\includepdfmacros. – Mico Apr 23 '12 at 17:36pdfpagesdocumentation, thepagecommandkey is executed on every page (or sheet of paper). You're interested in something like apagecommand*key that does not currently exist. As such, you need some other workaround. – Werner Apr 23 '12 at 17:41\begingroupand\endgroupstatements before and afer -- the\includepdfmergeand\includepdfstatements? This should keep the scope of the respectivepagecommanddirectives localized. (By default, the pagecommand statements apply to all pages...) – Mico Apr 23 '12 at 19:11