I've been using the Turtle skin for a long time and I'm starting to upgrade to Tiger but I have some problems with the settings.
On the album thumbnail page, with setting Sections/Folders/ Place captions above, the caption has no link and it is disruptive for the visitor to click, especially if the caption takes up a lot of space on the thumbnail. To make this page http://bruno.tredez.com/index.html work the way I want it to, I had to modify it by moving <div class="caption" and "comment"> into <a class="thumb" >.
For sub-albums I use the Turtle option: Location of thumbnails "As tooltip", but in Tiger there is only "Above" (with the previous problem) or "Below".
The 3 options the skin offers: "Over", "Below" and "Beside". I don't really see what is your problem. Naturally, when you place the thumbnail caption "Over" that works only with small captions. Large captions might cover most of the folder thumbnail. That's why 3 different options are offered.
Moving the caption inside a <a class="thumb"> container is a funny move. Why would you place the caption inside an element styled for the thumbnail? There's no guarantee, the code will work with this modification. No one expects that. The Title - in the <h3> tag - is linked to the subfolder. The comment isn't, because that can contain HTML formatting, and adding a link around a complex HTML is not allowed.
I've wrestled with this one, and I now take a "location specific" approach to it.
If the caption is displayed over a thumbnail, the whole caption - title and comment/description - is an active link. On a folder thumbnail it opens the folder, and on an image thumbnail it opens the lightbox (or the slide page, in the case of a "slide page" skin). In short, the captions have the same anchors as the thumbnail images themselves.
To avoid collisions, I strip all HTML tags out of the user-entered title and comment/description when they're used in this context. This does mean that they lose things like embedded bold and italic tags as well as embedded anchor strings, but that's just too bad.
For use elsewhere, like below a thumbnail or in the caption area of the lightbox, I leave the user-entered stuff alone.