She says she used a private server as a matter of convenience and to avoid having to carry two smartphones, one for work and one for personal use. The Blackberry supplied by the government could only handle one email address which would have been her work address. It appears she did not use or even activate her official government email account.
This is an issue because it meant that classified government secrets ended up on her private server. The security of her private server is very unlikely to have been as good as the security of the government's servers. It also gave her control over what should and should not be provided to the government, made public via freedom of information requests, passed on the Congressional committees, etc.
Clinton may be guilty of criminal offences relating to mishandling classified information, hence the FBI involvement. However, despite Trump and his supporters calling for her to be jailed, it is unlikely she would be convicted even if she was prosecuted. There would have to be something really explosive in the new emails to change that. She could, however, lose her security clearance. But, regardless of how unlikely it may be, this gives Trump and his supporters a chance to brand her a crook. He is, of course, going over the top. He has said this is "bigger than Watergate". It isn't.
Whether this will affect the outcome of the election is difficult to say at this stage. The timing is certainly unfortunate for Clinton.