No, I did not uncheck this box. I've checked again and emoticons are still enabled. Nor do I don't have any caching plugin installed.
Any emoticons that I typed manually prior to installing your plugin still work but everything after I installed and subsequently disabled the plugin shows up as the punctuation marks in my blog.
Basically, I installed the plugin and whenever I needed a smiley, I selected it from the speedy smiley box and it appeared as punctuation marks in the code. However, if I look at my post, the smiley was not there. If I deleted the punctuation marks and manually typed it in, it shows as punctuation marks in my actual blog post. As far as I can tell, the formatting/styling of my theme has not been affected.
I did not receive any error messages and no, I've not tried the slow method and if I am honest, I am reluctant to do so at this stage.