UserAgent: Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/59.0.3071.115 Safari/537.36

Steps to reproduce the problem:
If an SMIL animation makes an element invisible, then it intermittently affects the correct behaviour of the animation.

Consider the following sample: https://jsfiddle.net/0coeo4ef/

<svg width="500" height="500" viewBox="0 0 150 150">

   <image xlink:href="http://lorempixel.com/output/cats-q-c-30-30-1.jpg" height="30" width="30" x="80" y="100">
     <animate id="one" attributeName="x" begin="0s;three.end+2s" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="0s;three.end+2s" dur="1s" fill="freeze"
              from="100" to="100"/>
     <set attributeName="opacity" to="1" begin="0s;three.end+2s" fill="freeze"/>
     <set attributeName="opacity" to="0" begin="three.end+1s"/>
   </image>

   <image xlink:href="http://lorempixel.com/output/food-q-c-30-30-3.jpg" height="30" width="30" x="80" y="100"
          opacity="0">
     <animate id="two" attributeName="x" begin="one.end" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="one.end" dur="1s" fill="freeze"
              from="100" to="70"/>
     <set attributeName="opacity" to="1" begin="one.end" fill="freeze"/>
     <set attributeName="opacity" to="0" begin="three.end+1s"/>
   </image>

   <image xlink:href="http://lorempixel.com/output/people-q-c-30-30-3.jpg" height="30" width="30" x="80" y="100"
          opacity="0">
     <animate id="three" attributeName="x" begin="two.end" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="two.end" dur="1s" fill="freeze"
              from="100" to="40"/>
     <set attributeName="opacity" to="1" begin="two.end" fill="freeze"/>
     <set attributeName="opacity" to="0" begin="three.end+1s"/>
   </image>

</svg>

If you run this in Chrome 59, you should find that one of the images will intermittently not reappear when they are supposed. Sometimes it is the second image. Sometimes the third.  It's also non-deterministic. If you tweak the attributes a little - or the order of the <set> and <animate> elements, you can get a different result.

The same happens if you use visibility instead of opacity: https://jsfiddle.net/0coeo4ef/2/

<svg width="500" height="500" viewBox="0 0 150 150">

   <image xlink:href="http://lorempixel.com/output/cats-q-c-30-30-1.jpg" height="30" width="30" x="80" y="100">
     <animate id="one" attributeName="x" begin="0s;three.end+2s" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="0s;three.end+2s" dur="1s" fill="freeze"
              from="100" to="100"/>
     <set attributeName="visibility" to="visible" begin="0s;three.end+2s" fill="freeze"/>
     <set attributeName="visibility" to="hidden" begin="three.end+1s"/>
   </image>

   <image xlink:href="http://lorempixel.com/output/food-q-c-30-30-3.jpg" height="30" width="30" x="80" y="100"
          visibility="hidden">
     <animate id="two" attributeName="x" begin="one.end" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="one.end" dur="1s" fill="freeze"
              from="100" to="70"/>
     <set attributeName="visibility" to="visible" begin="one.end" fill="freeze"/>
     <set attributeName="visibility" to="hidden" begin="three.end+1s"/>
   </image>

   <image xlink:href="http://lorempixel.com/output/people-q-c-30-30-3.jpg" height="30" width="30" x="80" y="100"
          visibility="hidden">
     <animate id="three" attributeName="x" begin="two.end" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="two.end" dur="1s" fill="freeze"
              from="100" to="40"/>
     <set attributeName="visibility" to="visible" begin="two.end" fill="freeze"/>
     <set attributeName="visibility" to="hidden" begin="three.end+1s"/>
   </image>

</svg>

However if you don't go fully invisible (eg. opacity="0.1") everything seems to work perfectly: https://jsfiddle.net/0coeo4ef/1/

<svg width="500" height="500" viewBox="0 0 150 150">

   <image xlink:href="http://lorempixel.com/output/cats-q-c-30-30-1.jpg" height="30" width="30" x="80" y="100">
     <animate id="one" attributeName="x" begin="0s;three.end+2s" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="0s;three.end+2s" dur="1s" fill="freeze"
              from="100" to="100"/>
     <set attributeName="opacity" to="1" begin="0s;three.end+2s" fill="freeze"/>
     <set attributeName="opacity" to="0.1" begin="three.end+1s"/>
   </image>

   <image xlink:href="http://lorempixel.com/output/food-q-c-30-30-3.jpg" height="30" width="30" x="80" y="100"
          opacity="0.1">
     <animate id="two" attributeName="x" begin="one.end" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="one.end" dur="1s" fill="freeze"
              from="100" to="70"/>
     <set attributeName="opacity" to="1" begin="one.end" fill="freeze"/>
     <set attributeName="opacity" to="0.1" begin="three.end+1s"/>
   </image>

   <image xlink:href="http://lorempixel.com/output/people-q-c-30-30-3.jpg" height="30" width="30" x="80" y="100"
          opacity="0.1">
     <animate id="three" attributeName="x" begin="two.end" dur="1s" fill="freeze"
              from="80" to="100"/>
     <animate attributeName="y" begin="two.end" dur="1s" fill="freeze"
              from="100" to="40"/>
     <set attributeName="opacity" to="1" begin="two.end" fill="freeze"/>
     <set attributeName="opacity" to="0.1" begin="three.end+1s"/>
   </image>

</svg>

What is the expected behavior?
Elements should reappear at the same time as they begin to move across the canvas.

What went wrong?
Sometimes through the loop they don't reappear when they should.

Did this work before? N/A 

Does this work in other browsers? Yes

Chrome version: 59.0.3071.115  Channel: stable
OS Version: 6.1 (Windows 7, Windows Server 2008 R2)
Flash Version: 

Tweaking the timing of when we make the element visible doesn't seem to help at all.  For instance I tried having it reappear 0.1s before it starts moving, but the fault still happens.