Erratic behaviour, please help.

I'm experiencing the following, rather obscure behaviour and was wondering whether anyone out there could lend a kindly hand. This is the same for other progs but for explanation's sake I shall refer to my portable version of opera. The following is what happens in a series of scenarios:

1) Without using the portableapps menu I run opera from it's own folder off the usb drive (ie. "F:\Opera\"). I have my own mail/profile/bookmark settings stored in their respective subfolders (e.g. "F:\Opera\profile\) etc... and all works well.
OK SOO FAR, BUT READ ON.....

2) I drop the opera folder in the portableapps folder (ie "F:\PortableApps\Opera")
(i) Running the program from this folder directly, without use of portable apps menu, all my bookmarks, mail settings etc. are present as expected, no probs.

(ii) However, starting opera from the portableapps menu, none of these settings are present, my bookmarks etc.. have gone....odd...

Further new folders are created in the usb root directory (i.e. F:\default, F:\profile, F:\mail)...not ideal and rather messy having all these settings in the root folder, I delete these extra folders and start afresh.

(iii) From the portableapps menu I click 'Options->Install a New App' and select opera. Yippppeee, all my original bookmarks and mail settings are used and no random folders are created in the root directory.

(iv) HOWEVER, feeling rather chuffed at 'solving' my problem, I go ahead and setup another program with portableapps menu. It doesn't matter what program this is, but for an example I could setup Killbox, placing it in the folder: "F:\PortableApps\KillBox\", clicking 'Options->Install a New App'.

All seems ok, but when I now run opera from the portableapps menu, unless I redo the process of 'Options->Install a New App' and select opera again, I'm back to a slightly modified version of my original problem, with no bookmarks/mail settings and this time new folders being created in the Killbox directory!!!! (i.e. F:\Killbox\default, F:\Killbox\profile, F:\Killbox\mail).

Please someone, what's going on, it's a bit annoying to have to redo the 'Options->Install a New App' for opera everytime I set up a new app!

Thank you in advance for any advice.