While working with HeidiSQL, I run into this problem all the time, but I didn't get myself to report it so far.
To reproduce, create two simple tables:
CREATE TABLE a (id INT);
CREATE TABLE b (id INT);
(Depending on how you created them, update the tree to notify HeidiSQL of the new tables)
Then, in a query tab, enter the following:
select * from a,b where a.id=b.
After typing "a.", a dropdown list appears, showing the "id" field. Very good.
However, after typing "b.", HeidiSQL sends the following query to the server:
SHOW COLUMNS FROM a.id=b;
Which doesn't yield any usable results of course. If you add a space after the equals sign, it works:
select * from a,b where a.id= b. (note the extra space)