Can you ask questions about the changes? It sounds like what you really need is a critique partner: someone you can have a back-and-forth conversation with about changing your work in the direction you want.
I agree with everyone else too, especially the point `PinkyMcCoversong makes about holding off on submitting this anywhere for a while.
I'm just going to throw in that I agree with the above posters.
Also, if you're having this much trouble with proofreading feedback, maybe you should hold off a bit before putting this out. Get some critiques, revise, and then try and either ebook publish or submit to agents/editors. I feel like if you're this new, you should take your time to perfect your craft.
Well, I asked for a proofread mainly. Grammar and spelling as those are my weak points. But I feel the changes made have altered the tone of the character and the story a bit. It's little sentences here and there but kind of bugs me the more I read it. It's written in the style of journal, so that's probably the main issue I have with the tone. I don't know if it's the proofread job or if I just suck at writing and now with it cleaned up I see how bad I really am.
If it's grammatical and spelling errors that were fixed up and changed, I'd personally keep them. Grammar and spelling are extremely important and if you plan on or are getting this story published, you want it as polished as it can get.
Like ~Lytrigian asked, it would be more helpful to know if it was only proofread or if it got edited professionally (substantive editing and/or copy-editing). If changes have been made to your work and some suggestions offered for plot, etc., I would assume that it had been a substantive editing job (grammar and all that finalizing is usually copy-editing).
If it was simply a proofreading job, take the suggestions to heart and go through them. In the end, it's up to you if you want them to be made or not (as your work possibly will be going to an editor who will look it it again if you hire one before publishing), but it's good to consider them and see where they are coming from. If it's grammatical changes/spelling/structure, then it's best to probably accept them and keep them. If they are professional, they are hopefully knowledgeable of what they are doing.
If it was a professional editing job, however, changes may be more important to keep or talk to them about to find a solution that works for you and works for the story.
Version? Did you just get it proofread, or was it a professional edit? Proofreading and editing aren't the same things. A proofread shouldn't significantly change the work, just correct errors you missed.
I'd consider it part of a proofreader's job to correct the grammar of a 3rd person narrator and perhaps the dialogue of anyone who's supposed to be speaking in a formal register, but I wouldn't expect a lot of correction in casual dialogue where the characters may not be speaking grammatically.
Can you give an example of a change where you liked yours better, so we know the sort of thing you're talking about?