David,
Without looking at the emails and logs, it's hard to say why they're showing up in your junk folder. This could be caused by the spam checks that are being run on a system-level, any domain content filters that apply to your entire domain, or any content filters you configured for your own account. Go to Settings > My Settings > Filtering > Content Filtering. What do you have configured here? Check for anything that will move messages to the Junk E-mail folder and check those conditions against the messages you received.
You can also look at the message header for more information on spam weights. Go to the message in your junk folder, and in the content pane toolbar, click View > Header. If you look near the bottom, you'll see the TotalSpamWeight for that message. This can be an indication of whether the message was caught up in spam filtering. If you have a spam weight of 0, or something that indicates zero spam, the message is likely there because of a content filter. Now, it could be hard to determine what indicates the spam filter catching it, as the spam weights are subjective to the spam checks that are configured by the System Administrator, but it's a starting point.
Furthermore, if you go to Settings > My Settings > Filtering > Spam Filtering you'll see some more spam options. The Domain Administrator has the choice of allowing end users to adjust their spam weight actions. If they allow this, you'll see the option on the Options tab to "Override spam settings for this account". This will allow you to go to the Actions tab and adjust where messages with specific spam weights will go. Keep in mind, that the spam checks used to determine the weight are only configurable by the System Administrator, so you'd have to contact HostGator in regards to those. If you want, you can adjust these to Add Text to Subject. Doing this will send any messages that are determined to be spam to your inbox with a configurable message in front of the subject. If you have all spam being delivered to your inbox and you're still getting messages in your junk folder, you can scratch off the spam checks as the culprit.
I hope I was able to explain this a bit more for you and offer some useful suggestions. In the end, it will probably be quicker to get in contact with HostGator. They should be able to simply view the logs and headers and let you know what's going on with your messages. Best of luck!