update: found out what my cam is doing when the led is blinking and i cannot press anything: it is counting the pictures on the card. thats why in rec mode there is no delay (by the way, when you start in rec mode and then switch to playback, it still has this awful delay).how did i find this out? well, you cannot press buttons like "delete" or "menu", however you can cycle through the pictures and even press display button (to see histogram and stuff). when the led is blinking, the osd item that tells the number of the shown pictures (and how many pictures there are on the card) isnt shown. however when the led stops blinking, it is shown.
strange, as i thought looking it up in the "filetable" of the cards header is enough. i guess the cam is checking each picture to find out if it can render it? hmhm. will do some tests with defragmenting.
edit: defragmenting was of no use. even though i defragged for HOURS, i gained not even a second in startup delay.
but now i think i found the culprit: autoplay0.mrk (in MISC folder)
this file is created when you create a slideshow (in s3is you can keep up to three lists of predefined pictures that will be shown in a slideshow). this file was full of pictures that werent existing on the card anymore. i suspect the camera is searching the file and searching for the images mentioned in the file. the fact i had a lot of pics in that file that i already deleted sure was the missing bit of information in my case here. when i delete a picture in camera, the image is deleted from that "playlist" automatically. when i remove the pictures manually via cardreader, the file isnt updated ( i guess it is updated when you copy/move pictures using the canon tools like zoombrowser). anyhoo, deleting that file solved my problems.
now this still can be totally unrelated to your problem, especially when you dont own an s-series camera (although maybe DPOF can also be the culprit). however you say this problem only persists with CHDK enabled... hm.