Another Order Confirmation Problem

[xprotectrx]

I've seen there are many problem in here but I have a slightly different one.

Here is whats going on:
I get no order confirmation***(annoying problem, what I want to fix)/neither does a customer
I cannot do a tools>>send email to a customer
I turned on and DO get new account confirmations (so the email system is working in general)

What I did wrong:
My host one day did a bunch of changes and I freaked out because I wasn't getting order confirmations so I tried changing permissions and just general stuff you shouldn't do when things were working fine before.

Anyway, whats the best steps to fix this? Should I go in and replace the files / fix permissions on the files required to send the emails? I don't actually don't remember which ones those are anymore. Any help would be amazing!

[xprotectrx]

Dumb question #2, is this supposed to have a (1) after it when you do a 'tools>>send email' to a customer, or could this be part of the problem?
"Success Notice: Email sent to: xprotectrx##########################(1)"