My website has 4200 links from a single website, can that hurt my website`s reputation?

Selected answers from the Dumb SEO Questions Facebook & G+ community.

• 
  Ranu Jain: Hi Ashley,
  
  A few questions here:
  
  1) Which anchor text are you using for those 4200 links? Are these links sitewide?
  
  2) Have you recently made any changes related to those keywords?
  
  3) Are rankings same on google.com?
• 
  Ashley williams: Hi Ranu,
  
  1) These have been linked with a hyperlink on an image of my company's logo.
  
  2) I haven't made any changes to any of the keywords recently.
  
  3) Right now none of the keywords is ranked in Google (Both google.com and google.com.au)
• 
  Ranu Jain: Thanks Ashley. ;
  
  Why have you linked them to your site's logo? Ideally, your site's home page should be linked to the logo. ;
  
  So, you observed ranking fluctuations after you took these 4200 links? ;
  
  Could be possible that these links are hurting your site. Remove them or make them nofollow. ;
• 
  Dennis Suitters: You can also improve page loading by moving scripts to the bottom, and fix your Standards Compliancy by not using table for layout markup.
• 
  Ashley williams: Hi Ranu,
  
  I haven't linked them to my site's logo, the thing is that they have a small image slider across their website on the right sidebar in which they have placed my company's logo as I am their sponsor. Checkout this link http://www.sportingpulse.com/assoc_page.cgi?c=1-724-0-0-0&sID=160850&news_task=DETAIL&articleID=21777232. On the right sidebar you will see an image slider with my company's logo (MGB Accountants).
  
  My site's homepage is linked through their website. Earlier they were 3800 in number and at that time rankings were slowly improving but now its more than 4200 and I have lost all the rankings.
• 
  Ranu Jain: Ohk, ask them to make it nofollow. ;
• 
  Ashley williams: Hi Dennis,
  
  Did you take a look at my website. The point that you mentioned is in general or specifically for my website?
• 
  Dennis Suitters: Specifically for any site really. Using tables for layouts is a general no no. And placing scripts at the bottom of the page increases page load, as browsers tend to stop to execute scripts as they are loaded.
• 
  Ashley williams: Yes I understand that Dennis but there is no problem like that with my website. I have checked all the things and everything is fine. I am just not able to figure out why my website's ranking is not stable.
• 
  Dennis Suitters: It is strange, and I can't offer anything other than what others have already suggested.
• 
  Ovidiu Burduja: How do you track your rankings, Ashley? Some of the results you get are #personalised so it's best to use a third party / impartial #keyword #ranking #tool (google it).
• 
  Ashley williams: Hi Ovidio,
  
  Can you please tell me a bit more about personalized results.
• 
  W.E. Jonk: From the expert panel in this weeks SEO Questions hangout on air on 01:22:53 into the YouTube video: https://dumbseoquestions.com/q/my_website_has_4200_links_from_a_single_website_can_that_hurt_my_websites_reputation