Replaced/added some .apk's and they don't work?

I am using the dsixda kitchen to build ROMs for my Desire HD. I have built a few ROMs now and on the whole they have worked OK. However there area few apps that are out of date and a few I would like by default. I know I can download the majority of them from the market but I would like them just there by default. I know apps get updated all the time so I will never get perfection so bear with me.
I have sucessfully added ASTRO, HandyCalc, ROM Manager SMS Backup & Restore and VISIONary+ and these work fine. I have also updated the .apk's for Facebook to 1.8.1, Google Maps to 6.0.3, Twitter to 3.0.0, YouTube to 2.3.4 & GMail to 2.3.5.2.
Now heres my problem - If I try to update Adobe Reader to 10.1.1 by replacing the AdobeReader.apk with the latest one it doesn't work. Once the ROM is built and installed I can see the .apk is there in /system/app however there is no icon in All Apps for Adobe Reader and I can't open .pdf's.
I also use Google Goggles & Skype, however if I add these .apk's to the ROM they appear to be installed and start OK however Goggles crashes as soon as the camera is started from the app and Skype lets you run through the initial setup but then says the app needs reinstalling.

Is there something I am missing or are there apps that can't be updated and others that can't be included in ROMs?

Andy

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