As you have discovered, eScape doesn't embed fonts, but a bit of manual work would allow that - but that is not the answer for you.
If you are a tough, committed, ePub producer you can try IGP:FLIP
(Front List Interactive Publishing), which does everything, including embedding fonts if you have the nerve - there is a learning curve. You can give it a try here
. We are currently running it for free to debug and have a number of European language self-publishers using the beta version. One day we are thinking of a SaaS fee of $19.95 per month, but that is only on the drawing board, so use it while its free.
There are a number of tutorials which I suggest you go through to get the hang of it before jumping in, but it works like a rocket. We have 100 seats and 200 people creating advanced ePubs for major publishers around the world with this application every day, including highly customized, font-embedded books. If you feel you can use it, we can create you a custom portal to keep your content private.
There is no tutorial on font embedding at present so that is a bit mystical. After an initial look, if you are interested in giving it a try, we will put up a font embedding tutorial.
Since it is browser based, Mac and Win are fine if you are using Firefox or Safari (Safari is good because it displays embedded fonts in the Online QC mode). Of course IE anything doesn't work at this level of standards compliance so don't even try.
If you are doing Slovak all the time we can create a number of standard templates so you don't have to go through the embedding routine every time, it will happen automatically.
Anyway let me know if you are interested after a look.