1. a place where ships may ride secure from storms.  
2. a place secure from storms where ships may ride.  
3. a secure from storms place where ships may ride.  
4. a secure place where ships may ride from storms.  
5. a place secure where ships may ride from storms.  

Only 1. and 2. are grammatical.

Two matters are involved:

* *From storms* is a complement of the adjective *secure*—we speak of being secure **from** this or that threat. Moreover, it cannot act as a complement of *ride* as used in this context. When we speak of a ship *riding* we are ordinarily speaking of its position on the surface of the water; motion is not entailed (a ship may *ride* at anchor), and if motion **is** involved it is not 'voluntary' on the part of the ship: a ship does not 'ride' the waves as a man 'rides' a horse. 

 Semantically, then, 4. and 5. are excluded.

* With some exceptions<sup>&dagger;</sup>, adjectives precede their heads (the nominals they modify) which excludes 5. **But** there is an important exception: adjectivals with following modifiers or complements **must follow** their heads.

 Syntactically, then, 3. is excluded.  

 <sup>&dagger;</sup> <sub>The most common exception is participles; many of these routinely follow their heads&mdash;for example, *the man chosen*. Some linguists interpret these as reduced relative clauses, but I suspect the real cause is that such participles are frequently accompanied by following complements which would require postposition.</sub>

Both 1. and 2. are grammatical; but they do not mean the same thing. 

* In 1., it is the **ships** which are secure: *secure from storms* is a 'secondary complement' of *ride* which is attributed to its subject *ships*.

* In 2., it is the **place** which is secure. 

In this particular instance, which you use may make little difference to the ships; but it's easy enough to conceive a port where a storm leaves the ships unaffected but tears the roofs off all the buildings ashore!

ADDED:  

6. a place where ships secure from storms may ride

This is perfectly grammatical, but again it means something different from 1. (and 2.) Security now has nothing to do with the place: it's a restrictive adjunct describing the sorts of ships which may ride in the place. It implies that ships which cannot ride out a storm will not be permitted to enter the port!