Let me see if I got this straight...
You have 5 macros you use, with 1 being for each character. In the /castsequence you're finding that one macro's sequence use is affecting all the macros. That doesn't sound right and shouldn't be the case, UNLESS you're using a "/click" command to call them (Ualaa's response is interesting though, I would think thats only possible if both sequences were in the same macro... might need to test this later).


So something else might be causing this problem.
You mentioned keybinding examples "shift + #" (1-5) If you have this bound (i.e. keybindings), can you try changing the binding to just "1" and add [mod:shift] in the macro? If "1" is already being used by something else, you can combine macros like...

/use [nomod] pwnageSpell
/castsequence [mod:shift] heal, regen, bigheal, heal

Make sure whatever macro you're sharing that keybinding with has the [nomod], or "shift + #" will try to use both commands with you try to heal.

Also, you can use "reset=combat" instead of target (as Ualaa mentioned), to get the sequences back to the beginning after combat ends. This could also be the cause of your problems if the macros are getting used and not resetting correctly - which would cause spells to appear sharing the same command or appear to just be picking random spells in the sequence to cast.

Notes: Can use [mod:ctrl] and [mod:alt] as well or [nomod:shift] to exclude shift command.
If you want the option to reset a sequence in combat & out of combat, try "reset=combat/15" the " / " acts like 'or' if I recall correctly, so reset either 15 seconds of no use (combat state doesn't matter), or reset when combat ends.

If all else fails, go for broke & the lucky wheel of fortune with /castrandom smallHeal, bigHeal, Regen, Hearthstone