The online patcher doesn't account for headered/unheadered ROMs. It seems that Flips creates patches against unheadered ROMs behind the scenes. The online patcher doesn't support that, so you need to use unheadered ROMs with it instead.
I'm having trouble applying BPS patches to the SMW ROM I usually use, which is an .smc file. I tried changing it to an .sfc file, but it didn't work. I downloaded another SMW ROM from a different site, but I still get a "wrong imput file" prompt.
I don't know why people stopped making ppf patches for SM64 hacks. I try to patch an IPS patch to a CLEAN UNEXTENDED USA sm64 rom (what any tutorial says) and it says "this patch is not intended for this ROM"
Maybe I missed something but I can't play these hack for now...
EDIT : I found the solution, that's just because my rom wasn't a good dump while it was clean, I noticed that it didn't had a [!] next to it's name. Now it worked ! I let my message in case of people are in the same situation as me...
Can apply multiple patches at once. (Can't create multiple patches at once, though; make a batch file if you need that.)
Can apply and create BPS patches.
Generated IPS patches are (usually) (slightly) smaller (99.9994% on SMWCP2 1-15-13.ips) than those from LIPS. Both LIPS and Flips are fully capable of applying patches generated with the other.
Can apply and create patches through the command line. (Note that you'll get the C:\> prompt again, with Flips' output on top, if launched from cmd directly; it works fine from batch files. It's either that or flashing a console window for a tiny while when it's double clicked, and a rare bug is better than a common bug.)
Can apply a patch and run it in an emulator without forcing the user to create temporary files.
Can compile and run on any platform you want. You can get Windows or GTK+ GUIs, or a CLI-only app depending only on libc. (No plans for an OS X port; I don't have any Macs nearby, though I'll include it if someone else makes one.)
Can handle files containing characters outside the 8-bit character set (for example フローティング.ips). (But I'd bet you didn't even know LIPS can't handle that, they're rare.)
Refreshes all folder windows once file associations are claimed, instead of waiting until next reboot.
Open source, in case you care.
Despite the added features, the executable is smaller than LIPS. (Not that you have any reason to care.)
The important ones are the emulator launcher, BPS support (they're smaller than IPS, and can't be applied to wrong file), and the multi-patch support.