Caution windows keep popping up on my file and sometimes I'm unable to open it.

I have CS5 and began a file yesterday only to have multiple problems today when I tried to open it. First it said,
"File is not readable"
Yet when I opened it on my schools computer it was able to open. Then my other file did open but when I tried to save it it said,
"When spot colors are used with transparency,changing them to process colorsoutside of illustrator can generate unexpected results."
Then when I cancelled that it began to read,
"Saving to a legacy format may cause some changes to your text layout and disable some editing features when the document is read back in"
I don't really understand how I could fix this issue because obviously its the file inside. Now I did have a lot of imaged in the file that I made in photoshop where I took away the background, made it transparent then saved as a png. Is that the issue? How do I solve that? Most of my images on the file are .png and were edited with photoshop.
I would reaaallly appreciate someone helping me with this! I have no idea what to do!

"File is not readable" may have different reasons. One is that Illustrator doesn't like to open files directly from removable media. Of course there may also be issues with your hard disk, preferences problems or problems with fonts.
"Spot colors ...." is a never-ending-story. You should definitely read up on transparency and print production. Then decide if you need spot colors. On top of that this warns you of a condition that might never occur. This still applies to newer versions of Creative SUite: http://www.adobe.com/designcenter-archive/creativesuite/articles/cs3ip_transp.html
"Legacy format": you are using a newer version of Illustrator than the file has been created in. When downsaving you might lose editability of stuff you created in this session. But when not downsaving you might not be able to open the file on your home computer where you have an older version. Read the manual on how to save files.

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