I maintain applications, fix bugs, script, and create internal tools with HTML, CSS, Javascript, Jquery, Php, Mysql.
That sounds like development work to me.
Smaller organisations may not have a solid separation between IT administration and development - I've been in the same position before, myself, since we didn't have anyone with Ubuntu administration experience. Even now, I still help out sometimes, whenever the two IT admins are busy or on leave.
However, if the majority of your time is doing development work, then you are a developer. And it sounds to me like you are a PHP developer with what you write.
I don't use Java, C / C++ in my daily job... many devs around me seem to look down on me because I don't have that experience.
Unfortunately, there are some Java and C/C++ programmers who look down on web application developers who use PHP. There's a few reasons for this, some of them reasonably valid - but there are plenty of serious PHP developers who are extremely good at what they do, and it is used in a lot of large-scale sites.
I consider myself a developer, but I fear others may not based on me being part of IT - the untrue stereotype is that IT are just guys who install applications and image your computer, they don't code etc. Note that i disagree with this.
Would this inhibit my ability to become a developer?
Not really - when you apply for a new position, highlight the relevant experience - what you have done as a developer, what problems you have solved, what tools/frameworks you have used.
But don't completely neglect your IT experience - a developer with some IT admin skills (having a developer who knows how to run up an Ubuntu LAMP stack is invaluable in some teams) and customer interaction experience can be more valued than a developer who has only ever cut code. Just write it in a way so that you don't make your work as a developer appear subordinate to the IT side.
I'd like to not have to start as a entry level again, but move straight into the upper entry-level developer position... and eventually work remote :)
If you stick to looking for a job in the same toolset of PHP, MySQL, CSS, JavaScript, then you could probably look for a lower mid-level job after 2-3 years as an entry/junior developer. What will help is if you get yourself working on personal projects at home, or even get involved in an open-source project or two. There are plenty of small open-source projects on GitHub that are creating modules for the major frameworks (and experience in a framework like Laravel, Symfony, Zend, etc, is always a bonus).
If you want to jump over to Java or C/C++ - you may have to find a junior position somewhere sooner rather than later. You will also have to start learning that in your spare time.